Staphylococcus aureus polynucleotides and sequences

ABSTRACT

The present invention provides polynucleotide sequences of the genome of  Staphylococcus aureus,  polypeptide sequences encoded by the polynucleotide sequences, corresponding polynucleotides and polypeptides, vectors and hosts comprising the polynucleotides, and assays and other uses thereof. The present invention further provides polynucleotide and polypeptide sequence information stored on computer readable media, and computer-based systems and methods which facilitate its use.

CROSS REFERENCE TO RELATED APPLICATIONS

[0001] This application is a divisional of and claims priority under 35U.S.C. § 120 to U.S. application Ser. No. 08/956,171, filed Oct. 20,1997, which is a continuation-in-part of and claims priority under 35U.S.C. § 120 to U.S. application Ser. No. 08/781,986, filed Jan. 3,1997, which is a non-provisional of and claims benefit under 35 U.S.C. §119(e) of U.S. Provisional Application No. 60/009,861, filed Jan. 5,1996.

REFERENCE TO A SEQUENCE LISTING PROVIDED ON COMPACT DISC

[0002] This application refers to a “Sequence Listing”, which isprovided as an electronic document on two identical compact discs(CD-R), labeled “Copy 1” and “Copy 2.” These compact discs each containthe electronic document, filename “PB248P1D1 sequence listing.txt”(6,143,385 bytes in size, created on Dec. 23, 2002), which is herebyincorporated in its entirety herein.

FIELD OF THE INVENTION

[0003] The present invention relates to the field of molecular biology.In particular, it relates to, among other things, nucleotide sequencesof Staphylococcus aureus, contigs, ORFs, fragments, probes, primers andrelated polynucleotides thereof, peptides and polypeptides encoded bythe sequences, and uses of the polynucleotides and sequences thereof,such as in fermentation, polypeptide production, assays andpharmaceutical development, among others.

BACKGROUND OF THE INVENTION

[0004] The genus Staphylococcus includes at least 20 distinct species.(For a review see Novick, R. P., The Staphylococcus as a MolecularGenetic System, Chapter 1, pgs. 1-37 in MOLECULAR BIOLOGY OF THESTAPHYLOCOCCI, R. Novick, Ed., VCH Publishers, New York (1990)). Speciesdiffer from one another by 80% or more, by hybridization kinetics,whereas strains within a species are at least 90% identical by the samemeasure.

[0005] The species Staphylococcus aureus, a gram-positive, facultativelyaerobic, clump-forming cocci, is among the most important etiologicalagents of bacterial infection in humans, as discussed briefly below.

[0006] Human Health and S. Aureus

[0007]Staphylococcus aureus is a ubiquitous pathogen. (See, forinstance, Mims et al., MEDICAL MICROBIOLOGY, Mosby-Year Book EuropeLimited, London, UK (1993)). It is an etiological agent of a variety ofconditions, ranging in severity from mild to fatal. A few of the morecommon conditions caused by S. aureus infection are bums, cellulitis,eyelid infections, food poisoning, joint infections, neonatalconjunctivitis, osteomyelitis, skin infections, surgical woundinfection, scalded skin syndrome and toxic shock syndrome, some of whichare described further below.

[0008] Burns

[0009] Burn wounds generally are sterile initially. However, theygenerally compromise physical and immune barriers to infection, causeloss of fluid and electrolytes and result in local or generalphysiological dysfunction. After cooling, contact with viable bacteriaresults in mixed colonization at the injury site. Infection may berestricted to the non-viable debris on the bum surface (“eschar”), itmay progress into full skin infection and invade viable tissue below theeschar and it may reach below the skin, enter the lymphatic and bloodcirculation and develop into septicemia. S. aureus is among the mostimportant pathogens typically found in burn wound infections. It candestroy granulation tissue and produce severe septicemia.

[0010] Cellulitis

[0011] Cellulitis, an acute infection of the skin that expands from atypically superficial origin to spread below the cutaneous layer, mostcommonly is caused by S. aureus in conjunction with S. pyrogenes.Cellulitis can lead to systemic infection. In fact, cellulitis can beone aspect of synergistic bacterial gangrene. This condition typicallyis caused by a mixture of S. aureus and microaerophilic streptococci. Itcauses necrosis and treatment is limited to excision of the necrotictissue. The condition often is fatal.

[0012] Eyelid Infections

[0013]S. aureus is the cause of styes and of sticky eye” in neonates,among other eye infections. Typically such infections are limited to thesurface of the eye, and may occasionally penetrate the surface with moresevere consequences.

[0014] Food Poisoning

[0015] Some strains of S. aureus produce one or more of fiveserologically distinct, heat and acid stable enterotoxins that are notdestroyed by digestive process of the stomach and small intestine(enterotoxins A-E). Ingestion of the toxin, in sufficient quantities,typically results in severe vomiting, but not diarrhea. The effect doesnot require viable bacteria. Although the toxins are known, theirmechanism of action is not understood.

[0016] Joint Infections

[0017]S. aureus infects bone joints causing diseases such osteomyelitis.

[0018] Osteomyelitis

[0019]S. aureus is the most common causative agent of haematogenousosteomyelitis. The disease tends to occur in children and adolescentsmore than adults and it is associated with non-penetrating injuries tobones. Infection typically occurs in the long end of growing bone, henceits occurrence in physically immature populations. Most often, infectionis localized in the vicinity of sprouting capillary loops adjacent toepiphysial growth plates in the end of long, growing bones.

[0020] Skin Infections

[0021]S. aureus is the most common pathogen of such minor skininfections as abscesses and boils. Such infections often are resolved bynormal host response mechanisms, but they also can develop into severeinternal infections. Recurrent infections of the nasal passages plaguenasal carriers of S. aureus.

[0022] Surgical Wound Infections

[0023] Surgical wounds often penetrate far into the body. Infection ofsuch wound thus poses a grave risk to the patient. S. aureus is the mostimportant causative agent of infections in surgical wounds. S. aureus isunusually adept at invading surgical wounds; sutured wounds can beinfected by far fewer S. aureus cells then are necessary to causeinfection in normal skin. Invasion of surgical wound can lead to severeS. aureus septicemia. Invasion of the blood stream by S. aureus can leadto seeding and infection of internal organs, particularly heart valvesand bone, causing systemic diseases, such as endocarditis andosteomyelitis.

[0024] Scalded Skin Syndrome

[0025]S. aureus is responsible for “scalded skin syndrome” (also calledtoxic epidermal necrosis, Ritter's disease and Lyell's disease). Thisdiseases occurs in older children, typically in outbreaks caused byflowering of S. aureus strains produce exfoliation (also called scaldedskin syndrome toxin). Although the bacteria initially may infect only aminor lesion, the toxin destroys intercellular connections, spreadsepidermal layers and allows the infection to penetrate the outer layerof the skin, producing the desquamiation that typifies the diseases.Shedding of the outer layer of skin generally reveals normal skin below,but fluid lost in the process can produce severe injury in youngchildren if it is not treated properly.

[0026] Toxic Shock Syndrome

[0027] Toxic shock syndrome is caused by strains of S. aureus thatproduce the so-called toxic shock syndrome toxin. The disease can becaused by S. aureus infection at any site, but it is too oftenerroneously viewed exclusively as a disease solely of women who usetampons. The disease involves toxaemia and septicemia, and can be fatal.

[0028] Nocosomial Infections

[0029] In the 1984 National Nocosomial Infection Surveillance Study(“NNIS”) S. aureus was the most prevalent agent of surgical woundinfections in many hospital services, including medicine, surgery,obstetrics, pediatrics and newborns.

[0030] Resistance to Drugs of S. aureus Strains

[0031] Prior to the introduction of penicillin the prognosis forpatients seriously infected with S. aureus was unfavorable. Followingthe introduction of penicillin in the early 1940s even the worst S.aureus infections generally could be treated successfully. The emergenceof penicillin-resistant strains of S. aureus did not take long, however.Most strains of S. aureus encountered in hospital infections today donot respond to penicillin; although, fortunately, this is not the casefor S. aureus encountered in community infections.

[0032] It is well known now that penicillin-resistant strains of S.aureus produce a lactamase which converts penicillin to pencillinoicacid, and thereby destroys antibiotic activity. Furthermore, thelactamase gene often is propagated episomally, typically on a plasmid,and often is only one of several genes on an episomal element that,together, confer multidrug resistance.

[0033] Methicillins, introduced in the 1960s, largely overcame theproblem of penicillin resistance in S. aureus. These compounds conservethe portions of penicillin responsible for antibiotic activity andmodify or alter other portions that make penicillin a good substrate forinactivating lactamases. However, methicillin resistance has emerged inS. aureus, along with resistance to many other antibiotics effectiveagainst this organism, including aminoglycosides, tetracycline,chloramphenicol, macrolides and lincosamides. In fact,methicillin-resistant strains of S. aureus generally are multiply drugresistant.

[0034] The molecular genetics of most types of drug resistance in S.aureus has been elucidated (See Lyon et al., Microbiology Reviews 51:88-134 (1987)). Generally, resistance is mediated by plasmids, as notedabove regarding penicillin resistance; however, several stable forms ofdrug resistance have been observed that apparently involve integrationof a resistance element into the S. aureus genome itself.

[0035] Thus far each new antibiotic gives rise to resistance strains,stains emerge that are resistance to multiple drugs and increasinglypersistent forms of resistance begin to emerge. Drug resistance of S.aureus infections already poses significant treatment difficulties,which are likely to get much worse unless new therapeutic agents aredeveloped.

[0036] Molecular Genetics of Staphylococcus Aureus

[0037] Despite its importance in, among other things, human disease,relatively little is known about the genome of this organism.

[0038] Most genetic studies of S. aureus have been carried out using thestrain NCTC8325, which contains prophages psi11, psi12 and psi13, andthe UV-cured derivative of this strain, 8325-4 (also referred to asRN450), which is free of the prophages.

[0039] These studies revealed that the S. aureus genome, like that ofother staphylococci, consists of one circular, covalently closed,double-stranded DNA and a collection of so-called variable accessorygenetic elements, such as prophages, plasmids, transposons and the like.

[0040] Physical characterization of the genome has not been carried outin any detail. Pattee et al. published a low resolution and incompletegenetic and physical map of the chromosome of S. aureus strain NCTC8325. (Pattee et al. Genetic and Physical Mapping of Chromosome ofStaphylococcus aureus NCTC 8325, Chapter 11, pgs. 163-169 in MOLECULARBIOLOGY OF THE STAPHYLOCOCCI, R. P. Novick, Ed., VCH Publishers, NewYork, (1990) The genetic map largely was produced by mapping insertionsof Tn551 and Tn4001, which, respectively, confer erythromycin andgentamicin resistance, and by analysis of SmaI-digested DNA by PulsedField Gel Electrophoresis (“PFGE”).

[0041] The map was of low resolution; even estimating the physical sizeof the genome was difficult, according to the investigators. The size ofthe largest SmaI chromosome fragment, for instance, was too large foraccurate sizing by PFGE. To estimate its size, additional restrictionsites had to be introduced into the chromosome using a transposoncontaining a SmaI recognition sequence.

[0042] In sum, most physical characteristics and almost all of the genesof Staphylococcus aureus are unknown. Among the few genes that have beenidentified, most have not been physically mapped or characterized indetail. Only a very few genes of this organism have been sequenced.(See, for instance Thomsberry, J., Antimicrobial Chemotherapy 21 SupplC: 9-16 (1988), current versions of GENBANK and other nucleic aciddatabases, and references that relate to the genome of S. aureus such asthose set out elsewhere herein.)

[0043] It is clear that the etiology of diseases mediated or exacerbatedby S. aureus infection involves the programmed expression of S. aureusgenes, and that characterizing the genes and their patterns ofexpression would add dramatically to our understanding of the organismand its host interactions. Knowledge of S. aureus genes and genomicorganization would dramatically improve understanding of diseaseetiology and lead to improved and new ways of-preventing, ameliorating,arresting and reversing diseases. Moreover, characterized genes andgenomic fragments of S. aureus would provide reagents for, among otherthings, detecting, characterizing and controlling S. aureus infections.There is a need therefore to characterize the genome of S. aureus andfor polynucleotides and sequences of this organism.

SUMMARY OF THE INVENTION

[0044] The present invention is based on the sequencing of fragments ofthe Staphylococcus aureus genome. The primary nucleotide sequences whichwere generated are provided in SEQ ID NOS: 1-5,191.

[0045] The present invention provides the nucleotide sequence of severalthousand contigs of the Staphylococcus aureus genome, which are listedin tables below and set out in the Sequence Listing submitted herewith,and representative fragments thereof, in a form which can be readilyused, analyzed, and interpreted by a skilled artisan. In one embodiment,the present invention is provided as contiguous strings of primarysequence information corresponding to the nucleotide sequences depictedin SEQ ID NOS: 1-5,191.

[0046] The present invention further provides nucleotide sequences whichare at least 95% identical to the nucleotide sequences of SEQ ID NOS:1-5,191.

[0047] The nucleotide sequence of SEQ ID NOS: 1-5,191, a representativefragment thereof, or a nucleotide sequence which is at least 95%identical to the nucleotide sequence of SEQ ID NOS: 1-5,191 may beprovided in a variety of mediums to facilitate its use. In oneapplication of this embodiment, the sequences of the present inventionare recorded on computer readable media. Such media includes, but is notlimited to: magnetic storage media, such as floppy discs, hard discstorage medium, and magnetic tape; optical storage media such as CD-ROM;electrical storage media such as RAM and ROM; and hybrids of thesecategories such as magnetic/optical storage media.

[0048] The present invention further provides systems, particularlycomputer-based systems which contain the sequence information hereindescribed stored in a data storage means. Such systems are designed toidentify commercially important fragments of the Staphylococcus aureusgenome.

[0049] Another embodiment of the present invention is directed tofragments of the Staphylococcus aureus genome having particularstructural or functional attributes. Such fragments of theStaphylococcus aureus genome of the present invention include, but arenot limited to, fragments which encode peptides, hereinafter referred toas open reading frames or ORFs,” fragments which modulate the expressionof an operably linked ORF, hereinafter referred to as expressionmodulating fragments or EMFs,” and fragments which can be used todiagnose the presence of Staphylococcus aureus in a sample, hereinafterreferred to as diagnostic fragments or “DFs.”

[0050] Each of the ORFs in fragments of the Staphylococcus aureus genomedisclosed in Tables 1-3, and the EMFs found 5′ to the ORFs, can be usedin numerous ways as polynucleotide reagents. For instance, the sequencescan be used as diagnostic probes or amplification primers for detectingor determining the presence of a specific microbe in a sample, toselectively control gene expression in a host and in the production ofpolypeptides, such as polypeptides encoded by ORFs of the presentinvention, particular those polypeptides that have a pharmacologicalactivity.

[0051] The present invention further includes recombinant constructscomprising one or more fragments of the Staphylococcus aureus genome ofthe present invention. The recombinant constructs of the presentinvention comprise vectors, such as a plasmid or viral vector, intowhich a fragment of the Staphylococcus aureus has been inserted.

[0052] The present invention further provides host cells containing anyof the isolated fragments of the Staphylococcus aureus genome of thepresent invention. The host cells can be a higher eukaryotic host cell,such as a mammalian cell, a lower eukaryotic cell, such as a yeast cell,or a procaryotic cell such as a bacterial cell.

[0053] The present invention is further directed to isolatedpolypeptides and proteins encoded by ORFs of the present invention. Avariety of methods, well known to those of skill in the art, routinelymay be utilized to obtain any of the polypeptides and proteins of thepresent invention. For instance, polypeptides and proteins of thepresent invention having relatively short, simple amino acid sequencesreadily can be synthesized using commercially available automatedpeptide synthesizers. Polypeptides and proteins of the present inventionalso may be purified from bacterial cells which naturally produce theprotein. Yet another alternative is to purify polypeptide and proteinsof the present invention from cells which have been altered to expressthem.

[0054] The invention further provides polypeptides comprisingStaphylococcus aureus epitopes and vaccine compositions comprising suchpolypeptides. Also provided are methods for vaccinating an individualagainst Staphylococcus aureus infection.

[0055] The invention further provides methods of obtaining homologs ofthe fragments of the Staphylococcus aureus genome of the presentinvention and homologs of the proteins encoded by the ORFs of thepresent invention. Specifically, by using the nucleotide and amino acidsequences disclosed herein as a probe or as primers, and techniques suchas PCR cloning and colony/plaque hybridization, one skilled in the artcan obtain homologs.

[0056] The invention further provides antibodies which selectively bindpolypeptides and proteins of the present invention. Such antibodiesinclude both monoclonal and polyclonal antibodies.

[0057] The invention further provides hybridomas which produce theabove-described antibodies. A hybridoma is an immortalized cell linewhich is capable of secreting a specific monoclonal antibody.

[0058] The present invention further provides methods of identifyingtest samples derived from cells which express one of the ORFs of thepresent invention, or a homolog thereof. Such methods compriseincubating a test sample with one or more of the antibodies of thepresent invention, or one or more of the Dfs or antigens of the presentinvention, under conditions which allow a skilled artisan to determineif the sample contains the ORF or product produced therefrom.

[0059] In another embodiment of the present invention, kits are providedwhich contain the necessary reagents to carry out the above-describedassays.

[0060] Specifically, the invention provides a compartmentalized kit toreceive, in close confinement, one or more containers which comprises:(a) a first container comprising one of the antibodies, antigens, or oneof the DFs of the present invention; and (b) one or more othercontainers comprising one or more of the following: wash reagents,reagents capable of detecting presence of bound antibodies, antigens orhybridized DFs.

[0061] Using the isolated proteins of the present invention, the presentinvention further provides methods of obtaining and identifying agentscapable of binding to a polypeptide or protein encoded by one of theORFs of the present invention. Specifically, such agents include, asfurther described below, antibodies, peptides, carbohydrates,pharmaceutical agents and the like. Such methods comprise steps of:(a)contacting an agent with an isolated protein encoded by one of theORFs of the present invention; and (b)determining whether the agentbinds to said protein.

[0062] The present genomic sequences of Staphylococcus aureus will be ofgreat value to all laboratories working with this organism and for avariety of commercial purposes. Many fragments of the Staphylococcusaureus genome will be immediately identified by similarity searchesagainst GenBank or protein databases and will be of immediate value toStaphylococcus aureus researchers and for immediate commercial value forthe production of proteins or to control gene expression.

[0063] The methodology and technology for elucidating extensive genomicsequences of bacterial and other genomes has and will greatly enhancethe ability to analyze and understand chromosomal organization. Inparticular, sequenced contigs and genomes will provide the models fordeveloping tools for the analysis of chromosome structure and function,including the ability to identify genes within large segments of genomicDNA, the structure, position, and spacing of regulatory elements, theidentification of genes with potential industrial applications, and theability to do comparative genomic and molecular phylogeny.

BRIEF DESCRIPTION OF THE DRAWINGS

[0064]FIG. 1 is a block diagram of a computer system (102) that can beused to implement computer-based systems of present invention.

[0065]FIG. 2 is a schematic diagram depicting the data flow and computerprograms used to collect, assemble, edit and annotate the contigs of theStaphylococcus aureus genome of the present invention. Both Macintoshand Unix platforms are used to handle the AB 373 and 377 sequence datafiles, largely as described in Kerlavage et al., Proceedings of theTwenty-Sixth Annual Hawaii International Conference on System Sciences,585, IEEE Computer Society Press, Wash. D.C. (1993). Factura (AB) is aMacintosh program designed for automatic vector sequence removal andend-trimming of sequence files. The program Loadis runs on a Macintoshplatform and parses the feature data extracted from the sequence filesby Factura to the Unix based Staphylococcus aureus relational database.Assembly of contigs (and whole genome sequences) is accomplished byretrieving a specific set of sequence files and their associatedfeatures using extrseq, a Unix utility for retrieving sequences from anSQL database. The resulting sequence file is processed by seq_filter totrim portions of the sequences with more than 2% ambiguous nucleotides.The sequence files were assembled using TIGR Assembler, an assemblyengine designed at The Institute for Genomic Research (TIGR”) for rapidand accurate assembly of thousands of sequence fragments. The collectionof contigs generated by the assembly step is loaded into the databasewith the lassie program. Identification of open reading frames (ORFs) isaccomplished by processing contigs with zorf. The ORFs are searchedagainst S. aureus sequences from Genbank and against all proteinsequences using the BLASTN and BLASTP programs, described in Altschul etal., J. Mol. Biol. 215: 403-410 (1990)). Results of the ORFdetermination and similarity searching steps were loaded into thedatabase. As described below, some results of the determination and thesearches are set out in Tables 1-3.

DETAILED DESCRIPTION OF ILLUSTRATIVE EMBODIMENTS

[0066] The present invention is based on the sequencing of fragments ofthe Staphylococcus aureus genome and analysis of the sequences. Theprimary nucleotide sequences generated by sequencing the fragments areprovided in SEQ ID NOS: 1-5,191. (As used herein, the “primary sequence”refers to the nucleotide sequence represented by the IUPAC nomenclaturesystem.)

[0067] In addition to the aforementioned Staphylococcus aureuspolynucleotide and polynucleotide sequences, the present inventionprovides the nucleotide sequences of SEQ ID NOS: 1-5,191, orrepresentative fragments thereof, in a form which can be readily used,analyzed, and interpreted by a skilled artisan.

[0068] As used herein, a “representative fragment of the nucleotidesequence depicted in SEQ ID NOS: 1-5,191” refers to any portion of theSEQ ID NOS: 1-5,191 which is not presently represented within a publiclyavailable database. Preferred representative fragments of the presentinvention are Staphylococcus aureus open reading frames (ORFS”),expression modulating fragment (EMFs”) and fragments which can be usedto diagnose the presence of Staphylococcus aureus in sample (“DFs”). Anon-limiting identification of preferred representative fragments isprovided in Tables 1-3.

[0069] As discussed in detail below, the information provided in SEQ IDNOS: 1-5,191 and in Tables 1-3 together with routine cloning, synthesis,sequencing and assay methods will enable those skilled in the art toclone and sequence all “representative fragments” of interest, includingopen reading frames encoding a large variety of Staphylococcus aureusproteins.

[0070] While the presently disclosed sequences of SEQ ID NOS: 1-5,191are highly accurate, sequencing techniques are not perfect and, inrelatively rare instances, further investigation of a fragment orsequence of the invention may reveal a nucleotide sequence error presentin a nucleotide sequence disclosed in SEQ ID NOS: 1-5,191. However, oncethe present invention is made available (i.e., once the information inSEQ ID NOS: 1-5,191 and Tables 1-3 has been made available), resolving arare sequencing error in SEQ ID NOS: 1-5,191 will be well within theskill of the art. The present disclosure makes available sufficientsequence information to allow any of the described contigs or portionsthereof to be obtained readily by straightforward application of routinetechniques. Further sequencing of such polynucleotide may proceed inlike manner using manual and automated sequencing methods which areemployed ubiquitous in the art. Nucleotide sequence editing software ispublicly available. For example, Applied Biosystem's (AB) AutoAssemblercan be used as an aid during visual inspection of nucleotide sequences.By employing such routine techniques potential errors readily may beidentified and the correct sequence then may be ascertained by targetingfurther sequencing effort, also of a routine nature, to the regioncontaining the potential error.

[0071] Even if all of the very rare sequencing errors in SEQ ID NOS:1-5,191 were corrected, the resulting nucleotide sequences would stillbe at least 95% identical, nearly all would be at least 99% identical,and the great majority would be at least 99.9% identical to thenucleotide sequences of SEQ ID NOS: 1-5,191.

[0072] As discussed elsewhere herein, polynucleotides of the presentinvention readily may be obtained by routine application of well knownand standard procedures for cloning and sequencing DNA. Detailed methodsfor obtaining libraries and for sequencing are provided below, forinstance. A wide variety of Staphylococcus aureus strains that can beused to prepare S aureus genomic DNA for cloning and for obtainingpolynucleotides of the present invention are available to the publicfrom recognized depository institutions, such as the American TypeCulture Collection (ATCC”).

[0073] The nucleotide sequences of the genomes from different strains ofStaphylococcus aureus differ somewhat. However, the nucleotide sequencesof the genomes of all Staphylococcus aureus strains will be at least 95%identical, in corresponding part, to the nucleotide sequences providedin SEQ ID NOS: 1-5,191. Nearly all will be at least 99% identical andthe great majority will be 99.9% identical.

[0074] Thus, the present invention further provides nucleotide sequenceswhich are at least 95%, preferably 99% and most preferably 99.9%identical to the nucleotide sequences of SEQ ID NOS: 1-5,191, in a formwhich can be readily used, analyzed and interpreted by the skilledartisan.

[0075] Methods for determining whether a nucleotide sequence is at least95%, at least 99% or at least 99.9% identical to the nucleotidesequences of SEQ ID NOS: 1-5,191 are routine and readily available tothe skilled artisan. For example, the well known fasta algorithmdescribed in Pearson and Lipman, Proc. Natl. Acad. Sci. USA 85: 2444(1988) can be used to generate the percent identity of nucleotidesequences. The

[0076] BLASTN program also can be used to generate an identity score ofpolynucleotides compared to one another.

COMPUTER RELATED EMBODIMENTS

[0077] The nucleotide sequences provided in SEQ ID NOS: 1-5,191, arepresentative fragment thereof, or a nucleotide sequence at least 95%,preferably at least 96%, 97%, 98% or 99% and most preferably at least99.9% identical to a polynucleotide sequence of SEQ ID NOS: 1-5,191 maybe “provided” in a variety of mediums to facilitate use thereof. As usedherein, “provided” refers to a manufacture, other than an isolatednucleic acid molecule, which contains a nucleotide sequence of thepresent invention; i.e., a nucleotide sequence provided in SEQ ID NOS:1-5,191, a representative fragment thereof, or a nucleotide sequence atleast 95%, preferably at least 96%, 97%, 98% or 99% and most preferablyat least 99.9% identical to a polynucleotide of SEQ ID NOS: 1-5,191.Such a manufacture provides a large portion of the Staphylococcus aureusgenome and parts thereof (e.g., a Staphylococcus aureus open readingframe (ORF)) in a form which allows a skilled artisan to examine themanufacture using means not directly applicable to examining theStaphylococcus aureus genome or a subset thereof as it exists in natureor in purified form.

[0078] In one application of this embodiment, a nucleotide sequence ofthe present invention can be recorded on computer readable media. Asused herein, “computer readable media” refers to any medium which can beread and accessed directly by a computer. Such media include, but arenot limited to: magnetic storage media, such as floppy discs, hard discstorage medium, and magnetic tape; optical storage media such as CD-ROM;electrical storage media such as RAM and ROM; and hybrids of thesecategories, such as magnetic/optical storage media. A skilled artisancan readily appreciate how any of the presently known computer readablemediums can be used to create a manufacture comprising computer readablemedium having recorded thereon a nucleotide sequence of the presentinvention. Likewise, it will be clear to those of skill how additionalcomputer readable media that may be developed also can be used to createanalogous manufactures having recorded thereon a nucleotide sequence ofthe present invention.

[0079] As used herein, “recorded” refers to a process for storinginformation on computer readable medium. A skilled artisan can readilyadopt any of the presently know methods for recording information oncomputer readable medium to generate manufactures comprising thenucleotide sequence information of the present invention.

[0080] A variety of data storage structures are available to a skilledartisan for creating a computer readable medium having recorded thereona nucleotide sequence of the present invention. The choice of the datastorage structure will generally be based on the means chosen to accessthe stored information. In addition, a variety of data processorprograms and formats can be used to store the nucleotide sequenceinformation of the present invention on computer readable medium. Thesequence information can be represented in a word processing text file,formatted in commercially-available software such as WordPerfect andMicroSoft Word, or represented in the form of an ASCII file, stored in adatabase application, such as DB2, Sybase, Oracle, or the like. Askilled artisan can readily adapt any number of data-processorstructuring formats (e.g., text file or database) in order to obtaincomputer readable medium having recorded thereon the nucleotide sequenceinformation of the present invention.

[0081] Computer software is publicly available which allows a skilledartisan to access sequence information provided in a computer readablemedium. Thus, by providing in computer readable form the nucleotidesequences of SEQ ID NOS: 1-5,191, a representative fragment thereof, ora nucleotide sequence at least 95%, preferably at least 96%, 97%, 98% or99% and most preferably at least 99.9% identical to a sequence of SEQ IDNOS: 1-5,191 the present invention enables the skilled artisan routinelyto access the provided sequence information for a wide variety ofpurposes.

[0082] The examples which follow demonstrate how software whichimplements the BLAST (Altschul et al., J. Mol. Biol. 215:403-410 (1990))and BLAZE (Brutlag et al., Comp. Chem. 17:203-207 (1993)) searchalgorithms on a Sybase system was used to identify open reading frames(ORFs) within the Staphylococcus aureus genome which contain homology toORFs or proteins from both Staphylococcus aureus and from otherorganisms. Among the ORFs discussed herein are protein encodingfragments of the Staphylococcus aureus genome useful in producingcommercially important proteins, such as enzymes used in fermentationreactions and in the production of commercially useful metabolites.

[0083] The present invention further provides systems, particularlycomputer-based systems, which contain the sequence information describedherein. Such systems are designed to identify, among other things,commercially important fragments of the Staphylococcus aureus genome.

[0084] As used herein, “a computer-based system” refers to the hardwaremeans, software means, and data storage means used to analyze thenucleotide sequence information of the present invention. The minimumhardware means of the computer-based systems of the present inventioncomprises a central processing unit (CPU), input means, output means,and data storage means. A skilled artisan can readily appreciate thatany one of the currently available computer-based system are suitablefor use in the present invention.

[0085] As stated above, the computer-based systems of the presentinvention comprise a data storage means having stored therein anucleotide sequence of the present invention and the necessary hardwaremeans and software means for supporting and implementing a search means.

[0086] As used herein, “data storage means” refers to memory which canstore nucleotide sequence information of the present invention, or amemory access means which can access manufactures having recordedthereon the nucleotide sequence information of the present invention.

[0087] As used herein, “search means” refers to one or more programswhich are implemented on the computer- based system to compare a targetsequence or target structural motif with the sequence information storedwithin the data storage means. Search means are used to identifyfragments or regions of the present genomic sequences which match aparticular target sequence or target motif. A variety of knownalgorithms are disclosed publicly and a variety of commerciallyavailable software for conducting search means are and can be used inthe computer-based systems of the present invention. Examples of suchsoftware includes, but is not limited to, MacPattern (EMBL), BLASTN andBLASTX (NCBIA). A skilled artisan can readily recognize that any one ofthe available algorithms or implementing software packages forconducting homology searches can be adapted for use in the presentcomputer-based systems.

[0088] As used herein, a “target sequence” can be any DNA or amino acidsequence of six or more nucleotides or two or more amino acids. Askilled artisan can readily recognize that the longer a target sequenceis, the less likely a target sequence will be present as a randomoccurrence in the database. The most preferred sequence length of atarget sequence is from about 10 to 100 amino acids or from about 30 to300 nucleotide residues. However, it is well recognized that searchesfor commercially important fragments, such as sequence fragmentsinvolved in gene expression and protein processing, may be of shorterlength.

[0089] As used herein, “a target structural motif,” or “target motif,”refers to any rationally selected sequence or combination of sequencesin which the sequence(s) are chosen based on a three-dimensionalconfiguration which is formed upon the folding of the target motif.There are a variety of target motifs known in the art. Protein targetmotifs include, but are not limited to, enzymatic active sites andsignal sequences. Nucleic acid target motifs include, but are notlimited to, promoter sequences, hairpin structures and inducibleexpression elements (protein binding sequences).

[0090] A variety of structural formats for the input and output meanscan be used to input and output the information in the computer-basedsystems of the present invention. A preferred format for an output meansranks fragments of the Staphylococcus aureus genomic sequencespossessing varying degrees of homology to the target sequence or targetmotif. Such presentation provides a skilled artisan with a ranking ofsequences which contain various amounts of the target sequence or targetmotif and identifies the degree of homology contained in the identifiedfragment.

[0091] A variety of comparing means can be used to compare a targetsequence or target motif with the data storage means to identifysequence fragments of the Staphylococcus aureus genome. In the presentexamples, implementing software which implement the BLAST and BLAZEalgorithms, described in Altschul et al., J. Mol. Biol. 215: 403-410(1990), was used to identify open reading frames within theStaphylococcus aureus genome. A skilled artisan can readily recognizethat any one of the publicly available homology search programs can beused as the search means for the computer-based systems of the presentinvention. Of course, suitable proprietary systems that may be known tothose of skill also may be employed in this regard.

[0092]FIG. 1 provides a block diagram of a computer system illustrativeof embodiments of this aspect of present invention. The computer system102 includes a processor 106 connected to a bus 104. Also connected tothe bus 104 are a main memory 108 (preferably implemented as randomaccess memory, RAM) and a variety of secondary storage devices 110, suchas a hard drive 112 and a removable medium storage device 114. Theremovable medium storage device 114 may represent, for example, a floppydisk drive, a CD-ROM drive, a magnetic tape drive, etc. A removablestorage medium 116 (such as a floppy disk, a compact disk, a magnetictape, etc.) containing control logic and/or data recorded therein may beinserted into the removable medium storage device 114. The computersystem 102 includes appropriate software for reading the control logicand/or the data from the removable medium storage device 114, once it isinserted into the removable medium storage device 114.

[0093] A nucleotide sequence of the present invention may be stored in awell known manner in the main memory 108, any of the secondary storagedevices 110, and/or a removable storage medium 116. During execution,software for accessing and processing the genomic sequence (such assearch tools, comparing tools, etc.) reside in main memory 108, inaccordance with the requirements and operating parameters of theoperating system, the hardware system and the software program orprograms.

BIOCHEMICAL EMBODIMENTS

[0094] Other embodiments of the present invention are directed toisolated fragments of the Staphylococcus aureus genome. The fragments ofthe Staphylococcus aureus genome of the present invention include, butare not limited to fragments which encode peptides, hereinafter openreading frames (ORFs), fragments which modulate the expression of anoperably linked ORF, hereinafter expression modulating fragments (EMFs)and fragments which can be used to diagnose the presence ofStaphylococcus aureus in a sample, hereinafter diagnostic fragments(DFs).

[0095] As used herein, an “isolated nucleic acid molecule” or an“isolated fragment of the Staphylococcus aureus genome” refers to anucleic acid molecule possessing a specific nucleotide sequence whichhas been subjected to purification means to reduce, from thecomposition, the number of compounds which are normally associated withthe composition. Particularly, the term refers to the nucleic acidmolecules having the sequences set out in SEQ ID NOS: 1-5,191, torepresentative fragments thereof as described above, to polynucleotidesat least 95%, preferably at least 96%, 97%, 98% or 99% and especiallypreferably at least 99.9% identical in sequence thereto, also as set outabove.

[0096] A variety of purification means can be used to generated theisolated fragments of the present invention. These include, but are notlimited to methods which separate constituents of a solution based oncharge, solubility, or size.

[0097] In one embodiment, Staphylococcus aureus DNA can be mechanicallysheared to produce fragments of 15-20 kb in length. These fragments canthen be used to generate an Staphylococcus aureus library by insertingthem into lambda clones as described in the Examples below. Primersflanking, for example, an ORF, such as those enumerated in Tables 1-3can then be generated using nucleotide sequence information provided inSEQ ID NOS: 1-5,191. Well known and routine techniques of PCR cloningthen can be used to isolate the ORF from the lambda DNA library ofStaphylococcus aureus genomic DNA. Thus, given the availability of SEQID NOS: 1-5,191, the information in Tables 1, 2 and 3, and theinformation that may be obtained readily by analysis of the sequences ofSEQ ID NOS: 1-5,191 using methods set out above, those of skill will beenabled by the present disclosure to isolate any ORF-containing or othernucleic acid fragment of the present invention.

[0098] The isolated nucleic acid molecules of the present inventioninclude, but are not limited to single stranded and double stranded DNA,and single stranded RNA.

[0099] As used herein, an “open reading frame,” ORF, means a series oftriplets coding for amino acids without any termination codons and is asequence translatable into protein.

[0100] Tables 1, 2 and 3 list ORFs in the Staphylococcus aureus genomiccontigs of the present invention that were identified as putative codingregions by the GeneMark software using organism-specific second-orderMarkov probability transition matrices. It will be appreciated thatother criteria can be used, in accordance with well known analyticalmethods, such as those discussed herein, to generate more inclusive,more restrictive or more selective lists.

[0101] Table 1 sets out ORFs in the Staphylococcus aureus contigs of thepresent invention that are at least 80 amino acids long and over acontinuous region of at least 50 bases which are 95% or more identical(by BLAST analysis) to an S. aureus nucleotide sequence availablethrough Genbank in November 1996.

[0102] Table 2 sets out ORFs in the Staphylococcus aureus contigs of thepresent invention that are not in Table 1 and match, with a BLASTPprobability score of 0.01 or less, a polypeptide sequence availablethrough Genbank by September 1996.

[0103] Table 3 sets out ORFs in the Staphylococcus aureus contigs of thepresent invention that do not match significantly, by BLASTP analysis, apolypeptide sequence available through Genbank by September 1996.

[0104] In each table, the first and second columns identify the ORF by,respectively, contig number (SEQ ID NO) and ORF number within thecontig; the third column indicates the first nucleotide of the ORF,counting from the 5′ end of the contig strand shown in the sequencelisting; and the fifth column indicates the length of each ORF innucleotides. It will be appreciated that some ORFs are located on thereverse strand. The numbering identifying such ORFs also representsnucleotide positions counting from the 5′ end of the strand shown in thesequence listing.

[0105] In Tables 1 and 2, column five, lists the “match accession” forthe closest matching sequence available through Genbank. These referencenumbers are the databases entry numbers commonly used by those of skillin the art, who will be familiar with their denominators. Descriptionsof the nomenclature are available from the National Center forBiotechnology Information. Column six in Tables 1 and 2 provides the“gene name” of the matching sequence; column seven provides the BLAST“similarity”; column eight provides the BLAST “identity” score from thecomparison of the ORF and the homologous gene; and column nine indicatesthe length in nucleotides of the highest scoring “segment pair”identified by the BLAST identity analysis.

[0106] The concepts of percent identity and percent similarity of twopolypeptide sequences is well understood in the art. For example, twopolypeptides 10 amino acids in length which differ at three amino acidpositions (e.g., at positions 1, 3 and 5) are said to have a percentidentity of 70%. However, the same two polypeptides would be deemed tohave a percent similarity of 80% if, for example at position 5, theamino acids moieties, although not identical, were “similar” (i.e.,possessed similar biochemical characteristics). Many programs foranalysis of nucleotide or amino acid sequence similarity, such as fastaand BLAST specifically list percent identity of a matching region as anoutput parameter. Thus, for instance, Tables 1 and 2 herein enumeratethe percent identity “of the highest scoring segment pair” in each ORFand its listed relative. Further details concerning the algorithms andcriteria used for homology searches are provided below and are describedin the pertinent literature highlighted by the citations provided below.

[0107] It will be appreciated that other criteria can be used togenerate more inclusive and more exclusive listings of the types set outin the tables. As those of skill will appreciate, narrow and broadsearches both are useful. Thus, a skilled artisan can readily identifyORFs in contigs of the Staphylococcus aureus genome other than thoselisted in Tables 1-3, such as ORFs which are overlapping or encoded bythe opposite strand of an identified ORF in addition to thoseascertainable using the computer-based systems of the present invention.

[0108] As used herein, an “expression modulating fragment,” EMF, means aseries of nucleotide molecules which modulates the expression of anoperably linked ORF or EMF.

[0109] As used herein, a sequence is said to “modulate the expression ofan operably linked sequence” when the expression of the sequence isaltered by the presence of the EMF. EMFs include, but are not limitedto, promoters, and promoter modulating sequences (inducible elements).One class of EMFs are fragments which induce the expression or anoperably linked ORF in response to a specific regulatory factor orphysiological event.

[0110] EMF sequences can be identified within the contigs of theStaphylococcus aureus genome by their proximity to the ORFs provided inTables 1-3. An intergenic segment, or a fragment of the intergenicsegment, from about 10 to 200 nucleotides in length, taken from any oneof the ORFs of Tables 1-3 will modulate the expression of an operablylinked ORF in a fashion similar to that found with the naturally linkedORF sequence. As used herein, an “intergenic segment” refers tofragments of the Staphylococcus aureus genome which are between twoORF(s) herein described. EMFs also can be identified using known EMFs asa target sequence or target motif in the computer-based systems of thepresent invention. Further, the two methods can be combined and usedtogether.

[0111] The presence and activity of an EMF can be confirmed using an EMFtrap vector. An EMF trap vector contains a cloning site linked to amarker sequence. A marker sequence encodes an identifiable phenotype,such as antibiotic resistance or a complementing nutrition auxotrophicfactor, which can be identified or assayed when the EMF trap vector isplaced within an appropriate host under appropriate conditions. Asdescribed above, a EMF will modulate the expression of an operablylinked marker sequence. A more detailed discussion of various markersequences is provided below.

[0112] A sequence which is suspected as being an EMF is cloned in allthree reading frames in one or more restriction sites upstream from themarker sequence in the EMF trap vector. The vector is then transformedinto an appropriate host using known procedures and the phenotype of thetransformed host in examined under appropriate conditions. As describedabove, an EMF will modulate the expression of an operably linked markersequence.

[0113] As used herein, a “diagnostic fragment,” DF, means a series ofnucleotide molecules which selectively hybridize to Staphylococcusaureus sequences. DFs can be readily identified by identifying uniquesequences within contigs of the Staphylococcus aureus genome, such as byusing well-known computer analysis software, and by generating andtesting probes or amplification primers consisting of the DF sequence inan appropriate diagnostic format which determines amplification orhybridization selectivity.

[0114] The sequences falling within the scope of the present inventionare not limited to the specific sequences herein described, but alsoinclude allelic and species variations thereof. Allelic and speciesvariations can be routinely determined by comparing the sequencesprovided in SEQ ID NOS: 1-5,191, a representative fragment thereof, or anucleotide sequence at least 99% and preferably 99.9% identical to SEQID NOS: 1-5,191, with a sequence from another isolate of the samespecies.

[0115] Furthermore, to accommodate codon variability, the inventionincludes nucleic acid molecules coding for the same amino acid sequencesas do the specific ORFs disclosed herein. In other words, in the codingregion of an ORF, substitution of one codon for another which encodesthe same amino acid is expressly contemplated.

[0116] Any specific sequence disclosed herein can be readily screenedfor errors by resequencing a particular fragment, such as an ORF, inboth directions (i.e., sequence both strands). Alternatively, errorscreening can be performed by sequencing corresponding polynucleotidesof Staphylococcus aureus origin isolated by using part or all of thefragments in question as a probe or primer.

[0117] Each of the ORFs of the Staphylococcus aureus genome disclosed inTables 1, 2 and 3, and the EMFs found 5′ to the ORFs, can be used aspolynucleotide reagents in numerous ways. For example, the sequences canbe used as diagnostic probes or diagnostic amplification primers todetect the presence of a specific microbe in a sample, particularStaphylococcus aureus. Especially preferred in this regard are ORF suchas those of Table 3, which do not match previously characterizedsequences from other organisms and thus are most likely to be highlyselective for Staphylococcus aureus. Also particularly preferred areORFs that can be used to distinguish between strains of Staphylococcusaureus, particularly those that distinguish medically important strain,such as drug-resistant strains.

[0118] In addition, the fragments of the present invention, as broadlydescribed, can be used to control gene expression through triple helixformation or antisense DNA or RNA, both of which methods are based onthe binding of a polynucleotide sequence to DNA or RNA. Triplehelix-formation optimally results in a shut-off of RNA transcriptionfrom DNA, while antisense RNA hybridization blocks translation of anmRNA molecule into polypeptide. Information from the sequences of thepresent invention can be used to design antisense and triplehelix-forming oligonucleotides. Polynucleotides suitable for use inthese methods are usually 20 to 40 bases in length and are designed tobe complementary to a region of the gene involved in transcription, fortriple-helix formation, or to the mRNA itself, for antisense inhibition.Both techniques have been demonstrated to be effective in model systems,and the requisite techniques are well known and involve routineprocedures. Triple helix techniques are discussed in, for example, Leeet al., Nucl. Acids Res. 6: 3073 (1979); Cooney et al, Science 241: 456(1988); and Dervan et al., Science 251: 1360 (1991). Antisensetechniques in general are discussed in, for instance, Okano, J.Neurochem. 56: 560 (1991) and OLIGODEOXYNUCLEOTIDES AS ANTISENSEINHIBITORS OF GENE EXPRESSION, CRC Press, Boca Raton, Fla. (1988)).

[0119] The present invention further provides recombinant constructscomprising one or more fragments of the Staphylococcus aureus genomicfragments and contigs of the present invention. Certain preferredrecombinant constructs of the present invention comprise a vector, suchas a plasmid or viral vector, into which a fragment of theStaphylococcus aureus genome has been inserted, in a forward or reverseorientation. In the case of a vector comprising one of the ORFs of thepresent invention, the vector may further comprise regulatory sequences,including for example, a promoter, operably linked to the ORF. Forvectors comprising the EMFs of the present invention, the vector mayfurther comprise a marker sequence or heterologous ORF operably linkedto the EMF.

[0120] Large numbers of suitable vectors and promoters are known tothose of skill in the art and are commercially available for generatingthe recombinant constructs of the present invention. The followingvectors are provided by way of example. Useful bacterial vectors includephagescript, PsiX174, pBluescript SK and KS (+and −), pNH8a, pNH16a,pNH18a, pNH46a (available from Stratagene); pTrc99A, pKK223-3, pKK233-3,pDR540, pRIT5 (available from Pharmacia). Useful eukaryotic vectorsinclude pWLneo, pSV2cat, pOG44, pXT1, pSG (available from Stratagene)pSVK3, pBPV, pMSG, pSVL (available from Pharmacia).

[0121] Promoter regions can be selected from any desired gene using CAT(chloramphenicol transferase) vectors or other vectors with selectablemarkers. Two appropriate vectors are pKK232-8 and pCM7. Particular namedbacterial promoters include lacI, lacZ, T3, T7, gpt, lambda PR, and trc.Eukaryotic promoters include CMV immediate early, HSV thymidine kinase,early and late SV40, LTRs from retrovirus, and mouse metallothionein-I.Selection of the appropriate vector and promoter is well within thelevel of ordinary skill in the art.

[0122] The present invention further provides host cells containing anyone of the isolated fragments of the Staphylococcus aureus genomicfragments and contigs of the present invention, wherein the fragment hasbeen introduced into the host cell using known methods. The host cellcan be a higher eukaryotic host cell, such as a mammalian cell, a lowereukaryotic host cell, such as a yeast cell, or a procaryotic cell, suchas a bacterial cell.

[0123] A polynucleotide of the present invention, such as a recombinantconstruct comprising an ORF of the present invention, may be introducedinto the host by a variety of well established techniques that arestandard in the art, such as calcium phosphate transfection, DEAE,dextran mediated transfection and electroporation, which are describedin, for instance, Davis, L. et al., BASIC METHODS IN MOLECULAR BIOLOGY(1986).

[0124] A host cell containing one of the fragments of the Staphylococcusaureus genomic fragments and contigs of the present invention, can beused in conventional manners to produce the gene product encoded by theisolated fragment (in the case of an ORF) or can be used to produce aheterologous protein under the control of the EMF.

[0125] The present invention further provides isolated polypeptidesencoded by the nucleic acid fragments of the present invention or bydegenerate variants of the nucleic acid fragments of the presentinvention. By “degenerate variant” is intended nucleotide fragmentswhich differ from a nucleic acid fragment of the present invention(e.g., an ORF) by nucleotide sequence but, due to the degeneracy of theGenetic Code, encode an identical polypeptide sequence.

[0126] Preferred nucleic acid fragments of the present invention are theORFs depicted in Tables 2 and 3 which encode proteins.

[0127] A variety of methodologies known in the art can be utilized toobtain any one of the isolated polypeptides or proteins of the presentinvention. At the simplest level, the amino acid sequence can besynthesized using commercially available peptide synthesizers. This isparticularly useful in producing small peptides and fragments of largerpolypeptides. Such short fragments as may be obtained most readily bysynthesis are useful, for example, in generating antibodies against thenative polypeptide, as discussed further below.

[0128] In an alternative method, the polypeptide or protein is purifiedfrom bacterial cells which naturally produce the polypeptide or protein.One skilled in the art can readily employ well-known methods forisolating polypeptides and proteins to isolate and purify polypeptidesor proteins of the present invention produced naturally by a bacterialstrain, or by other methods. Methods for isolation and purification thatcan be employed in this regard include, but are not limited to,immunochromatography, HPLC, size-exclusion chromatography, ion-exchangechromatography, and immuno-affinity chromatography.

[0129] The polypeptides and proteins of the present invention also canbe purified from cells which have been altered to express the desiredpolypeptide or protein. As used herein, a cell is said to be altered toexpress a desired polypeptide or protein when the cell, through geneticmanipulation, is made to produce a polypeptide or protein which itnormally does not produce or which the cell normally produces at a lowerlevel. Those skilled in the art can readily adapt procedures forintroducing and expressing either recombinant or synthetic sequencesinto eukaryotic or prokaryotic cells in order to generate a cell whichproduces one of the polypeptides or proteins of the present invention.

[0130] Any host/vector system can be used to express one or more of theORFs of the present invention. These include, but are not limited to,eukaryotic hosts such as HeLa cells, CV-1 cell, COS cells, and Sf9cells, as well as prokaryotic host such as E. coli and B. subtilis. Themost preferred cells are those which do not normally express theparticular polypeptide or protein or which expresses the polypeptide orprotein at low natural level.

[0131] “Recombinant,” as used herein, means that a polypeptide orprotein is derived from recombinant (e.g., microbial or mammalian)expression systems. “Microbial” refers to recombinant polypeptides orproteins made in bacterial or fungal (e.g., yeast) expression systems.As a product, “recombinant microbial” defines a polypeptide or proteinessentially free of native endogenous substances and unaccompanied byassociated native glycosylation. Polypeptides or proteins expressed inmost bacterial cultures, e.g., E. coli, will be free of glycosylationmodifications; polypeptides or proteins expressed in yeast will have aglycosylation pattern different from that expressed in mammalian cells.

[0132] “Nucleotide sequence” refers to a heteropolymer ofdeoxyribonucleotides. Generally, DNA segments encoding the polypeptidesand proteins provided by this invention are assembled from fragments ofthe Staphylococcus aureus genome and short oligonucleotide linkers, orfrom a series of oligonucleotides, to provide a synthetic gene which iscapable of being expressed in a recombinant transcriptional unitcomprising regulatory elements derived from a microbial or viral operon.

[0133] “Recombinant expression vehicle or vector” refers to a plasmid orphage or virus or vector, for expressing a polypeptide from a DNA (RNA)sequence. The expression vehicle can comprise a transcriptional unitcomprising an assembly of (1) a genetic regulatory elements necessaryfor gene expression in the host, including elements required to initiateand maintain transcription at a level sufficient for suitable expressionof the desired polypeptide, including, for example, promoters and, wherenecessary, an enhancers and a polyadenylation signal; (2) a structuralor coding sequence which is transcribed into mRNA and translated intoprotein, and (3) appropriate signals to initiate translation at thebeginning of the desired coding region and terminate translation at itsend. Structural units intended for use in yeast or eukaryotic expressionsystems preferably include a leader sequence enabling extracellularsecretion of translated protein by a host cell. Alternatively, whererecombinant protein is expressed without a leader or transport sequence,it may include an N-terminal methionine residue. This residue may or maynot be subsequently cleaved from the expressed recombinant protein toprovide a final product.

[0134] “Recombinant expression system” means host cells which havestably integrated a recombinant transcriptional unit into chromosomalDNA or carry the recombinant transcriptional unit extra chromosomally.The cells can be prokaryotic or eukaryotic. Recombinant expressionsystems as defined herein will express heterologous polypeptides orproteins upon induction of the regulatory elements linked to the DNAsegment or synthetic gene to be expressed.

[0135] Mature proteins can be expressed in mammalian cells, yeast,bacteria, or other cells under the control of appropriate promoters.Cell-free translation systems can also be employed to produce suchproteins using RNAs derived from the DNA constructs of the presentinvention. Appropriate cloning and expression vectors for use withprokaryotic and eukaryotic hosts are described in Sambrook et al.,MOLECULAR CLONING:A LABORATORY MANUAL, 2^(nd) Edition, Cold SpringHarbor Laboratory Press, Cold Spring Harbor, N.Y. (1989), the disclosureof which is hereby incorporated by reference in its entirety.

[0136] Generally, recombinant expression vectors will include origins ofreplication and selectable markers permitting transformation of the hostcell, e.g., the ampicillin resistance gene of E. coli and S. cerevisiaeTRPI gene, and a promoter derived from a highly expressed gene to directtranscription of a downstream structural sequence. Such promoters can bederived from operons encoding glycolytic enzymes such as3-phosphoglycerate kinase (PGK), alpha-factor, acid phosphatase, or heatshock proteins, among others. The heterologous structural sequence isassembled in appropriate phase with translation initiation andtermination sequences, and preferably, a leader sequence capable ofdirecting secretion of translated protein into the periplasmic space orextracellular medium. Optionally, the heterologous sequence can encode afusion protein including an N-terminal identification peptide impartingdesired characteristics, e.g., stabilization or simplified purificationof expressed recombinant product.

[0137] Useful expression vectors for bacterial use are constructed byinserting a structural DNA sequence encoding a desired protein togetherwith suitable translation initiation and termination signals in operablereading phase with a functional promoter. The vector will comprise oneor more phenotypic selectable markers and an origin of replication toensure maintenance of the vector and, when desirable, provideamplification within the host.

[0138] Suitable prokaryotic hosts for transformation include strains ofStaphylococcus aureus, E. coli, B. subtilis, Salmonella typhimurium andvarious species within the genera Pseudomonas, Streptomyces, andStaphylococcus. Others may, also be employed as a matter of choice.

[0139] As a representative but non-limiting example, useful expressionvectors for bacterial use can comprise a selectable marker and bacterialorigin of replication derived from commercially available plasmidscomprising genetic elements of the well known cloning vector pBR322(ATCC 37017). Such commercial vectors include, for example, pKK223-3(available form Pharmacia Fine Chemicals, Uppsala, Sweden) and GEM 1(available from Promega Biotec, Madison, Wis., USA). These pBR322“backbone” sections are combined with an appropriate promoter and thestructural sequence to be expressed.

[0140] Following transformation of a suitable host strain and growth ofthe host strain to an appropriate cell density, the selected promoter,where it is inducible, is derepressed or induced by appropriate means(e.g., temperature shift or chemical induction) and cells are culturedfor an additional period to provide for expression of the induced geneproduct. Thereafter cells are typically harvested, generally bycentrifugation, disrupted to release expressed protein, generally byphysical or chemical means, and the resulting crude extract is retainedfor further purification.

[0141] Various mammalian cell culture systems can also be employed toexpress recombinant protein. Examples of mammalian expression systemsinclude the COS-7 lines of monkey kidney fibroblasts, described inGluzman, Cell 23: 175 (1981), and other cell lines capable of expressinga compatible vector, for example, the C127, 3T3, CHO, HeLa and BHK celllines.

[0142] Mammalian expression vectors will comprise an origin ofreplication, a suitable promoter and enhancer, and also any necessaryribosome binding sites, polyadenylation site, splice donor and acceptorsites, transcriptional termination sequences, and 5′ flankingnontranscribed sequences. DNA sequences derived from the SV40 viralgenome, for example, SV40 origin, early promoter, enhancer, splice, andpolyadenylation sites may be used to provide the required nontranscribedgenetic elements.

[0143] Recombinant polypeptides and proteins produced in bacterialculture is usually isolated by initial extraction from cell pellets,followed by one or more salting-out, aqueous ion exchange or sizeexclusion chromatography steps. Microbial cells employed in expressionof proteins can be disrupted by any convenient method, includingfreeze-thaw cycling, sonication, mechanical disruption, or use of celllysing agents. Protein refolding steps can be used, as necessary, incompleting configuration of the mature protein. Finally, highperformance liquid chromatography (HPLC) can be employed for finalpurification steps.

[0144] An additional aspect of the invention includes Staphylococcusaureus polypeptides which are useful as immunodiagnostic antigens and/orimmunoprotective vaccines, collectively “immunologically usefulpolypeptides”. Such immunologically useful polypeptides may be selectedfrom the ORFs disclosed herein based on techniques well known in the artand described elsewhere herein. The inventors have used the followingcriteria to select several immunologically useful polypeptides:

[0145] As is known in the art, an amino terminal type I signal sequencedirects a nascent protein across the plasma and outer membranes to theexterior of the bacterial cell. Such outer membrane polypeptides areexpected to be immunologically useful. According to Izard, J. W. et al.,Mol. Microbiol. 13, 765-773; (1994), polypeptides containing type Isignal sequences contain the following physical attributes: The lengthof the type I signal sequence is approximately 15 to 25 primarilyhydrophobic amino acid residues with a net positive charge in theextreme amino terminus; the central region of the signal sequence mustadopt an alpha-helical conformation in a hydrophobic environment; andthe region surrounding the actual site of cleavage is ideally sixresidues long, with small side-chain amino acids in the −1 and −3positions.

[0146] Also known in the art is the type IV signal sequence which is anexample of the several types of functional signal sequences which existin addition to the type I signal sequence detailed above. Althoughfunctionally related, the type IV signal sequence possesses a unique setof biochemical and physical attributes (Strom, M. S. and Lory, S., J.Bacteriol. 174, 7345-7351; 1992)). These are typically six to eightamino acids with a net basic charge followed by an additional sixteen tothirty primarily hydrophobic residues. The cleavage site of a type IVsignal sequence is typically after the initial six to eight amino acidsat the extreme amino terminus. In addition, all type IV signal sequencescontain a phenylalanine residue at the +1 site relative to the cleavagesite.

[0147] Studies of the cleavage sites of twenty-six bacterial lipoproteinprecursors has allowed the definition of a consensus amino acid sequencefor lipoprotein cleavage. Nearly three-fourths of the bacteriallipoprotein precursors examined contained the sequence L-(A,S)-(G,A)-Cat positions −3 to +1, relative to the point of cleavage (Hayashi, S.and Wu, H. C. Lipoproteins in bacteria. J Bioenerg. Biomembr. 22,451-471; 1990).

[0148] It is well known that most anchored proteins found on the surfaceof gram-positive bacteria possess a highly conserved carboxy terminalsequence. More than fifty such proteins from organisms such as S.pyogenes, S. mutans, E. faecalis, S. pneumoniae, and others, have beenidentified based on their extracellular location and carboxy terminalamino acid sequence (Fischetti, V. A. Gram-positive commensal bacteriadeliver antigens to elicit mucosal and systemic immunity. ASM News 62,405-410; 1996). The conserved region is comprised of six charged aminoacids at the extreme carboxy terminus coupled to 15-20 hydrophobic aminoacids presumed to function as a transmembrane domain. Immediatelyadjacent to the transmembrane domain is a six amino acid sequenceconserved in nearly all proteins examined. The amino acid sequence ofthis region is L-P-X-G-X (SEQ ID NO:5256), where X is any amino acid.

[0149] Amino acid sequence similarities to proteins of known function byBLAST enables the assignment of putative functions to novel amino acidsequences and allows for the selection of proteins thought to functionoutside the cell wall. Such proteins are well known in the art andinclude “lipoprotein”, “periplasmic”, or “antigen”.

[0150] An algorithm for selecting antigenic and immunogenicStaphylococcus aureus polypeptides including the foregoing criteria wasdeveloped by the present inventors. Use of the algorithm by theinventors to select immunologically useful Staphylococcus aureuspolypeptides resulted in the selection of several ORFs which arepredicted to be outer membrane-associated proteins. These proteins areidentified below, and shown in the Sequence Listing as SEQ ID NOS: 5,192to 5,255. Thus the amino acid sequence of each of several antigenicStaphylococcus aureus polypeptides can be determined, for example, bylocating the amino acid sequence of the ORF in the Sequence Listing.Likewise the polynucleotide sequence encoding each ORF can be found bylocating the corresponding polynucleotide SEQ ID in Tables 1, 2, or 3,and finding the corresponding nucleotide sequence in the sequencelisting.

[0151] As will be appreciated by those of ordinary skill in the art,although a polypeptide representing an entire ORF may be the closestapproximation to a protein found in vivo, it is not always technicallypractical to express a complete ORF in vitro. It may be very challengingto express and purify a highly hydrophobic protein by common laboratorymethods. As a result, the immunologically useful polypeptides describedherein as SEQ ID NOS: 5,192-5,255 may have been modified slightly tosimplify the production of recombinant protein, and are the preferredembodiments. In general, nucleotide sequences which encode highlyhydrophobic domains, such as those found at the amino terminal signalsequence, are excluded for enhanced in vitro expression of thepolypeptides. Furthermore, any highly hydrophobic amino acid sequencesoccurring at the carboxy terminus are also excluded. Such truncatedpolypeptides include for example the mature forms of the polypeptidesexpected to exist in nature.

[0152] Those of ordinary skill in the art can identify soluble portionsthe polypeptide, and in the case of truncated polypeptides sequencesshown as SEQ ID NOS: 5,192-5,255, may obtain the complete predictedamino acid sequence of each polypeptide by translating the correspondingpolynucleotides sequences of the corresponding ORF listed in Tables 1,2and 3 and found in the sequence listing.

[0153] Accordingly, polypeptides comprising the complete amino acidsequence of an immunologically useful polypeptide selected from thegroup of polypeptides encoded by the ORFs shown as SEQ ID NOS:5,192-5,255, or an amino acid sequence at least 95% identical thereto,preferably at least 97% identical thereto, and most preferably at least99% identical thereto form an embodiment of the invention; in addition,polypeptides comprising an amino acid sequence selected from the groupof amino acid sequences shown in the sequence listing as SEQ ID NOS:5,191-5,255, or an amino acid sequence at least 95% identical thereto,preferably at least 97% identical thereto and most preferably 99%identical thereto, form an embodiment of the invention. Polynucleotidesencoding the foregoing polypeptides also form part of the invention.

[0154] In another aspect, the invention provides a peptide orpolypeptide comprising an epitope-bearing portion of a polypeptide ofthe invention, particularly those epitope-bearing portions (antigenicregions) identified in the sequence listing as SEQ ID NOS: 5,191-5,255.The epitope-bearing portion is an immunogenic or antigenic epitope of apolypeptide of the invention. An “immunogenic epitope” is defined as apart of a protein that elicits an antibody response when the wholeprotein is the immunogen. On the other hand, a region of a proteinmolecule to which an antibody can bind is defined as an “antigenicepitope.” The number of immunogenic epitopes of a protein generally isless than the number of antigenic epitopes. See, for instance, Geysen etal., Proc. Natl. Acad. Sci. USA 81:3998-4002 (1983).

[0155] As to the selection of peptides or polypeptides bearing anantigenic epitope (i.e., that contain a region of a protein molecule towhich an antibody can bind), it is well known in that art thatrelatively short synthetic peptides that mimic part of a proteinsequence are routinely capable of eliciting an antiserum that reactswith the partially mimicked protein. See, for instance, Sutcliffe, J.G., Shinnick, T. M., Green, N. and Learner, R. A. (1983) “Antibodiesthat react with predetermined sites on proteins”, Science, 219:660-666.Peptides capable of eliciting protein-reactive sera are frequentlyrepresented in the primary sequence of a protein, can be characterizedby a set of simple chemical rules, and are confined neither toimmunodominant regions of intact proteins (i.e., immunogenic epitopes)nor to the amino or carboxyl terminals.

[0156] Antigenic epitope-bearing peptides and polypeptides of theinvention are therefore useful to raise antibodies, including monoclonalantibodies, that bind specifically to a polypeptide of the invention.See, for instance, Wilson et al., Cell 37:767-778 (1984) at 777.

[0157] Antigenic epitope-bearing peptides and polypeptides of theinvention preferably contain a sequence of at least seven, morepreferably at least nine and most preferably between about 15 to about30 amino acids contained within the amino acid sequence of a polypeptideof the invention. Non-limiting examples of antigenic polypeptides orpeptides that can be used to generate S. aureus specific antibodiesinclude: a polypeptide comprising peptides shown below. Thesepolypeptide fragments have been determined to bear antigenic epitopes ofindicated S. aureus proteins by the analysis of the Jameson-Wolfantigenic index, a representative sample of which is shown in FIG. 3.

[0158] The epitope-bearing peptides and polypeptides of the inventionmay be produced by any conventional means. See, e.g., Houghten, R. A.(1985) General method for the rapid solid-phase synthesis of largenumbers of peptides: specificity of antigen-antibody interaction at thelevel of individual amino acids. Proc. Natl. Acad. Sci. USA82:5131-5135; this “Simultaneous Multiple Peptide Synthesis (SMPS)”process is further described in U.S. Pat. No. 4,631,211 to Houghten etal. (1986).

[0159] Epitope-bearing peptides and polypeptides of the invention areused to induce antibodies according to methods well known in the art.See, for instance, Sutcliffe et al., supra; Wilson et al., supra; Chow,M. et al., Proc. Natl. Acad. Sci. USA 82:910-914; and Bittle, F. J. etal., J. Gen. Virol. 66:2347-2354 (1985). Immunogenic epitope-bearingpeptides of the invention, i.e., those parts of a protein that elicit anantibody response when the whole protein is the immunogen, areidentified according to methods known in the art. See, for instance,Geysen et al., supra. Further still, U.S. Pat. No. 5,194,392 to Geysen(1990) describes a general method of detecting or determining thesequence of monomers (amino acids or other compounds) which is atopological equivalent of the epitope (i.e., a “mimotope”) which iscomplementary to a particular paratope (antigen binding site) of anantibody of interest. More generally, U.S. Pat. No. 4,433,092 to Geysen(1989) describes a method of detecting or determining a sequence ofmonomers which is a topographical equivalent of a ligand which iscomplementary to the ligand binding site of a particular receptor ofinterest. Similarly, U.S. Pat. No. 5,480,971 to Houghten, R. A. et al.(1996) on Peralkylated Oligopeptide Mixtures discloses linearC1-C7-alkyl peralkylated oligopeptides and sets and libraries of suchpeptides, as well as methods for using such oligopeptide sets andlibraries for determining the sequence of a peralkylated oligopeptidethat preferentially binds to an acceptor molecule of interest. Thus,non-peptide analogs of the epitope-bearing peptides of the inventionalso can be made routinely by these methods.

[0160] Immunologically useful polypeptides may be identified by analgorithm which locates novel Staphylococcus aureus outer membraneproteins, as is described above. Also listed are epitopes or “antigenicregions” of each of the identified polypeptides. The antigenic regions,or epitopes, are delineated by two numbers x-y, where x is the number ofthe first amino acid in the open reading frame included within theepitope and y is the number of the last amino acid in the open readingframe included within the epitope. For example, the first epitope in ORF168-6 is comprised of amino acids 36 to 45 of SEQ ID NO: 5,192. Theinventors have identified several epitopes for each of the antigenicpolypeptides identified. Accordingly, forming part of the presentinvention are polypeptides comprising an amino acid sequence of one ormore antigenic regions identified. The invention further providespolynucleotides encoding such polypeptides.

[0161] The present invention further includes isolated polypeptides,proteins and nucleic acid molecules which are substantially equivalentto those herein described. As used herein, substantially equivalent canrefer both to nucleic acid and amino acid sequences, for example amutant sequence, that varies from a reference sequence by one or moresubstitutions, deletions, or additions, the net effect of which does notresult in an adverse functional dissimilarity between reference andsubject sequences. For purposes of the present invention, sequenceshaving equivalent biological activity, and equivalent expressioncharacteristics are considered substantially equivalent. For purposes ofdetermining equivalence, truncation of the mature sequence should bedisregarded.

[0162] The invention further provides methods of obtaining homologs fromother strains of Staphylococcus aureus, of the fragments of theStaphylococcus aureus genome of the present invention and homologs ofthe proteins encoded by the ORFs of the present invention. As usedherein, a sequence or protein of Staphylococcus aureus is defined as ahomolog of a fragment of the Staphylococcus aureus fragments or contigsor a protein encoded by one of the ORFs of the present invention, if itshares significant homology to one of the fragments of theStaphylococcus aureus genome of the present invention or a proteinencoded by one of the ORFs of the present invention. Specifically, byusing the sequence disclosed herein as a probe or as primers, andtechniques such as PCR cloning and colony/plaque hybridization, oneskilled in the art can obtain homologs.

[0163] As used herein, two nucleic acid molecules or proteins are saidto “share significant homology” if the two contain regions which possessgreater than 85% sequence (amino acid or nucleic acid) homology.Preferred homologs in this regard are those with more than 90% homology.Especially preferred are those with 93% or more homology. Amongespecially preferred homologs those with 95% or more homology areparticularly preferred. Very particularly preferred among these arethose with 97% and even more particularly preferred among those arehomologs with 99% or more homology. The most preferred homologs amongthese are those with 99.9% homology or more. It will be understood that,among measures of homology, identity is particularly preferred in thisregard.

[0164] Region specific primers or probes derived from the nucleotidesequence provided in SEQ ID NOS: 1-5,191 or from a nucleotide sequenceat least 95%, particularly at least 99%, especially at least 99.5%identical to a sequence of SEQ ID NOS: 1-5,191 can be used to prime DNAsynthesis and PCR amplification, as well as to identify coloniescontaining cloned DNA encoding a homolog. Methods suitable to thisaspect of the present invention are well known and have been describedin great detail in many publications such as, for example, Innis et al.,PCR PROTOCOLS, Academic Press, San Diego, Calif. (1990)).

[0165] When using primers derived from SEQ ID NOS: 1-5,191 or from anucleotide sequence having an aforementioned identity to a sequence ofSEQ ID NOS: 1-5,191, one skilled in the art will recognize that byemploying high stringency conditions (e.g., annealing at 50-60° C. in 6×SSPC and 50% formamide, and washing at 50-65° C. in 0.5× SSPC) onlysequences which are greater than 75% homologous to the primer will beamplified. By employing lower stringency conditions (e.g., hybridizingat 35-37° C. in 5× SSPC and 40-45% formamide, and washing at 42° C. in0.5× SSPC), sequences which are greater than 40-50% homologous to theprimer will also be amplified.

[0166] When using DNA probes derived from SEQ ID NOS: 1-5,191, or from anucleotide sequence having an aforementioned identity to a sequence ofSEQ ID NOS: 1-5,191, for colony/plaque hybridization, one skilled in theart will recognize that by employing high stringency conditions (e.g.,hybridizing at 50-65° C. in 5× SSPC and 50% formamide, and washing at50-65° C. in 0.5× SSPC), sequences having regions which are greater than90% homologous to the probe can be obtained, and that by employing lowerstringency conditions (e.g., hybridizing at 35-37° C. in 5× SSPC and40-45% formamide, and washing at 42° C. in 0.5× SSPC), sequences havingregions which are greater than 35-45% homologous to the probe will beobtained.

[0167] Any organism can be used as the source for homologs of thepresent invention so long as the organism naturally expresses such aprotein or contains genes encoding the same. The most preferred organismfor isolating homologs are bacterias which are closely related toStaphylococcus aureus.

ILLUSTRATIVE USES OF COMPOSITIONS OF THE INVENTION

[0168] Each ORF provided in Tables 1 and 2 is identified with a functionby homology to a known gene or polypeptide. As a result, one skilled inthe art can use the polypeptides of the present invention forcommercial, therapeutic and industrial purposes consistent with the typeof putative identification of the polypeptide. Such identificationspermit one skilled in the art to use the Staphylococcus aureus ORFs in amanner similar to the known type of sequences for which theidentification is made; for example, to ferment a particular sugarsource or to produce a particular metabolite. A variety of reviewsillustrative of this aspect of the invention are available, includingthe following reviews on the industrial use of enzymes, for example,BIOCHEMICAL ENGINEERING AND BIOTECHNOLOGY HANDBOOK, 2^(nd) Ed.,Macmillan Publications, Ltd. NY (1991) and BIOCATALYSTS IN ORGANICSYNTHESES, Tramper et al., Eds., Elsevier Science Publishers, Amsterdam,The Netherlands (1985). A variety of exemplary uses that illustrate thisand similar aspects of the present invention are discussed below.

[0169] 1. Biosynthetic Enzymes

[0170] Open reading frames encoding proteins involved in mediating thecatalytic reactions involved in intermediary and macromolecularmetabolism, the biosynthesis of small molecules, cellular processes andother functions includes enzymes involved in the degradation of theintermediary products of metabolism, enzymes involved in centralintermediary metabolism, enzymes involved in respiration, both aerobicand anaerobic, enzymes involved in fermentation, enzymes involved in ATPproton motor force conversion, enzymes involved in broad regulatoryfunction, enzymes involved in amino acid synthesis, enzymes involved innucleotide synthesis, enzymes involved in cofactor and vitaminsynthesis, can be used for industrial biosynthesis.

[0171] The various metabolic pathways present in Staphylococcus aureuscan be identified based on absolute nutritional requirements as well asby examining the various enzymes identified in Table 1-3 and SEQ ID NOS:1-5,191.

[0172] Of particular interest are polypeptides involved in thedegradation of intermediary metabolites as well as non-macromolecularmetabolism. Such enzymes include amylases, glucose oxidases, andcatalase.

[0173] Proteolytic enzymes are another class of commercially importantenzymes. Proteolytic enzymes find use in a number of industrialprocesses including the processing of flax and other vegetable fibers,in the extraction, clarification and depectinization of fruit juices, inthe extraction of vegetables' oil and in the maceration of fruits andvegetables to give unicellular fruits. A detailed review of theproteolytic enzymes used in the food industry is provided in Rombouts etal., Symbiosis 21: 79 (1986) and Voragen et al. in BIOCATALYSTS INAGRICULTURAL BIOTECHNOLOGY, Whitaker et al., Eds., American ChemicalSociety Symposium Series 389: 93 (1989).

[0174] The metabolism of sugars is an important aspect of the primarymetabolism of Staphylococcus aureus. Enzymes involved in the degradationof sugars, such as, particularly, glucose, galactose, fructose andxylose, can be used in industrial fermentation. Some of the importantsugar transforming enzymes, from a commercial viewpoint, include sugarisomerases such as glucose isomerase. Other metabolic enzymes have foundcommercial use such as glucose oxidases which produces ketogulonic acid(KGA). KGA is an intermediate in the commercial production of ascorbicacid using the Reichstein's procedure, as described in Krueger et al.,Biotechnology 6(A), Rhine et al., Eds., Verlag Press, Weinheim, Germany(1984).

[0175] Glucose oxidase (GOD) is commercially available and has been usedin purified form as well as in an immobilized form for the deoxygenationof beer. See, for instance, Hartmeir et al., Biotechnology Letters 1: 21(1979). The most important application of GOD is the industrial scalefermentation of gluconic acid. Market for gluconic acids which are usedin the detergent, textile, leather, photographic, pharmaceutical, food,feed and concrete industry, as described, for example, in Bigelis etal., beginning on page 357 in GENE MANIPULATIONS AND FUNGI; Benett etal., Eds., Academic Press, New York (1985). In addition to industrialapplications, GOD has found applications in medicine for quantitativedetermination of glucose in body fluids recently in biotechnology foranalyzing syrups from starch and cellulose hydrosylates. Thisapplication is described in Owusu et al., Biochem. et Biophysica. Acta.872: 83 (1986), for instance.

[0176] The main sweetener used in the world today is sugar which comesfrom sugar beets and sugar cane. In the field of industrial enzymes, theglucose isomerase process shows the largest expansion in the markettoday. Initially, soluble enzymes were used and later immobilizedenzymes were developed (Krueger et al., Biotechnology, The Textbook ofIndustrial Microbiology, Sinauer Associated Incorporated, Sunderland,Mass. (1990)). Today, the use of glucose- produced high fructose syrupsis by far the largest industrial business using immobilized enzymes. Areview of the industrial use of these enzymes is provided by Jorgensen,Starch 40:307 (1988).

[0177] Proteinases, such as alkaline serine proteinases, are used asdetergent additives and thus represent one of the largest volumes ofmicrobial enzymes used in the industrial sector. Because of theirindustrial importance, there is a large body of published andunpublished information regarding the use of these enzymes in industrialprocesses. (See Faultman et al., Acid Proteases Structure Function andBiology, Tang, J., ed., Plenum Press, New York (1977) and Godfrey etal., Industrial Enzymes, MacMillan Publishers, Surrey, UK (1983) andHepner et al, Report Industrial Enzymes by 1990, Hel Hepner &Associates, London (1986)).

[0178] Another class of commercially usable proteins of the presentinvention are the microbial lipases, described by, for instance, Macraeet al., Philosophical Transactions of the Chiral Society of London310:227 (1985) and Poserke, Journal of the American Oil Chemist Society61:1758 (1984). A major use of lipases is in the fat and oil industryfor the production of neutral glycerides using lipase catalyzedinter-esterification of readily available triglycerides. Application oflipases include the use as a detergent additive to facilitate theremoval of fats from fabrics in the course of the washing procedures.

[0179] The use of enzymes, and in particular microbial enzymes, ascatalyst for key steps in the synthesis of complex organic molecules isgaining popularity at a great rate. One area of great interest is thepreparation of chiral intermediates. Preparation of chiral intermediatesis of interest to a wide range of synthetic chemists particularly thosescientists involved with the preparation of new pharmaceuticals,agrochemicals, fragrances and flavors. (See Davies et al., RecentAdvances in the Generation of Chiral Intermediates Using Enzymes, CRCPress, Boca Raton, Fla. (1990)). The following reactions catalyzed byenzymes are of interest to organic chemists: hydrolysis of carboxylicacid esters, phosphate esters, amides and nitriles, esterificationreactions, trans-esterification reactions, synthesis of amides,reduction of alkanones and oxoalkanates, oxidation of alcohols tocarbonyl compounds, oxidation of sulfides to sulfoxides, and carbon bondforming reactions such as the aldol reaction.

[0180] When considering the use of an enzyme encoded by one of the ORFsof the present invention for biotransformation and organic synthesis itis sometimes necessary to consider the respective advantages anddisadvantages of using a microorganism as opposed to an isolated enzyme.Pros and cons of using a whole cell system on the one hand or anisolated partially purified enzyme on the other hand, has been describedin detail by Bud et al., Chemistry in Britain (1987), p. 127.

[0181] Amino transferases, enzymes involved in the biosynthesis andmetabolism of amino acids, are useful in the catalytic production ofamino acids. The advantages of using microbial based enzyme systems isthat the amino transferase enzymes catalyze the stereo- selectivesynthesis of only L-amino acids and generally possess uniformly highcatalytic rates. A description of the use of amino transferases foramino acid production is provided by Roselle-David, Methods ofEnzymology 136:479 (1987).

[0182] Another category of useful proteins encoded by the ORFs of thepresent invention include enzymes involved in nucleic acid synthesis,repair, and recombination. A variety of commercially important enzymeshave previously been isolated from members of Staphylococcus aureus.These include Sau3A and Sau96I.

[0183] 2. Generation of Antibodies

[0184] As described here, the proteins of the present invention, as wellas homologs thereof, can be used in a variety procedures and methodsknown in the art which are currently applied to other proteins. Theproteins of the present invention can further be used to generate anantibody which selectively binds the protein. Such antibodies can beeither monoclonal or polyclonal antibodies, as well fragments of theseantibodies, and humanized forms.

[0185] The invention further provides antibodies which selectively bindto one of the proteins of the present invention and hybridomas whichproduce these antibodies. A hybridoma is an immortalized cell line whichis capable of secreting a specific monoclonal antibody.

[0186] In general, techniques for preparing polyclonal and monoclonalantibodies as well as hybridomas capable of producing the desiredantibody are well known in the art (Campbell, A. M., MONOCLONAL ANTIBODYTECHNOLOGY: LABORATORY TECHNIQUES IN BIOCHEMISTRY AND MOLECULAR BIOLOGY,Elsevier Science Publishers, Amsterdam, The Netherlands (1984); St.Groth et al., J. Immunol. Methods 35: 1-21 (1980), Kohler and Milstein,Nature 256: 495-497 (1975)), the trioma technique, the human B-cellhybridoma technique (Kozbor et al., Immunology Today-4: 72 (1983), pgs.77-96 of Cole et al., in MONOCLONAL ANTIBODIES AND CANCER THERAPY, AlanR. Liss, Inc. (1985)).

[0187] Any animal (mouse, rabbit, etc.) which is known to produceantibodies can be immunized with the pseudogene polypeptide. Methods forimmunization are well known in the art. Such methods includesubcutaneous or interperitoneal injection of the polypeptide. Oneskilled in the art will recognize that the amount of the protein encodedby the ORF of the present invention used for immunization will varybased on the animal which is immunized, the antigenicity of the peptideand the site of injection.

[0188] The protein which is used as an immunogen may be modified oradministered in an adjuvant in order to increase the protein'santigenicity. Methods of increasing the antigenicity of a protein arewell known in the art and include, but are not limited to coupling theantigen with a heterologous protein (such as globulin or galactosidase)or through the inclusion of an adjuvant during immunization.

[0189] For monoclonal antibodies, spleen cells from the immunizedanimals are removed, fused with myeloma cells, such as SP2/0-Ag14myeloma cells, and allowed to become monoclonal antibody producinghybridoma cells.

[0190] Any one of a number of methods well known in the art can be usedto identify the hybridoma cell which produces an antibody with thedesired characteristics. These include screening the hybridomas with anELISA assay, western blot analysis, or radioimmunoassay (Lutz et al.,Exp. Cell Res. 175: 109-124 (1988)).

[0191] Hybridomas secreting the desired antibodies are cloned and theclass and subclass is determined using procedures known in the art(Campbell, A. M., Monoclonal Antibody Technology: Laboratory Techniquesin Biochemistry and Molecular Biology, Elsevier Science Publishers,Amsterdam, The Netherlands (1984)).

[0192] Techniques described for the production of single chainantibodies (U.S. Pat. No. 946,778) can be adapted to produce singlechain antibodies to proteins of the present invention.

[0193] For polyclonal antibodies, antibody containing antisera isisolated from the immunized animal and is screened for the presence ofantibodies with the desired specificity using one of the above-describedprocedures.

[0194] The present invention further provides the above- describedantibodies in detectably labeled form. Antibodies can be detectablylabeled through the use of radioisotopes, affinity labels (such asbiotin, avidin, etc.), enzymatic labels (such as horseradish peroxidase,alkaline phosphatase, etc.) fluorescent labels (such as FITC orrhodamine, etc.), paramagnetic atoms, etc. Procedures for accomplishingsuch labeling are well-known in the art, for example see Stemberger etal., J. Histochem. Cytochem. 18:315 (1970); Bayer, E. A. et al., Meth.Enzym. 62:308 (1979); Engval, E. et al., Immunol. 109-129 (1972);Goding, J. W. J. Immunol. Meth. 13:215 (1976)).

[0195] The labeled antibodies of the present invention can be used forin vitro, in vivo, and in situ assays to identify cells or tissues inwhich a fragment of the Staphyococcus aureus genome is expressed.

[0196] The present invention further provides the above-describedantibodies immoblized on a solid support. Examples of such solidsupports include plastics such as polycarbonate, complex carbohydratessuch as agarose and sepharose, acrylic resins and such as polyacrylamideand latex beads. Techniques for coupling antibodies to such solidsupports are well known in the art (Weir, D. M. et al., “Handbook ofExperimental Immunology” 4th Ed., Blackwell Scientific Publications,Oxford, England, Chapter 10 (1986); Jacoby, W. D. et al., Meth. Enzym.34 Academic Press, N.Y. (1974)). The immobilized antibodies of thepresent invention can be used for in vitro, in vivo, and in situ assaysas well as for immunoaffinity purification of the proteins of thepresent invention.

[0197] 3. Diagnostic Assays and Kits

[0198] The present invention further provides methods to identify theexpression of one of the ORFs of the present invention, or homologthereof, in a test sample, using one of the DFs, antigens or antibodiesof the present invention.

[0199] In detail, such methods comprise incubating a test sample withone or more of the antibodies, or one or more of the DFs, or one or moreantigens of the present invention and assaying for binding of the DFs,antigens or antibodies to components within the test sample.

[0200] Conditions for incubating a DF, antigen or antibody with a testsample vary. Incubation conditions depend on the format employed in theassay, the detection methods employed, and the type and nature of the DFor antibody used in the assay. One skilled in the art will recognizethat any one of the commonly available hybridization, amplification orimmunological assay formats can readily be adapted to employ the Dfs,antigens or antibodies of the present invention. Examples of such assayscan be found in Chard, T., An Introduction to Radioimmunoassay andRelated Techniques, Elsevier Science Publishers, Amsterdam, TheNetherlands (1986); Bullock, G. R. et al., Techniques ininmunocytochemistry, Academic Press, Orlando, Fla. Vol. 1 (1982), Vol. 2(1983), Vol. 3 (1985); Tijssen, P., Practice and Theory of EnzymeImmunoassays: Laboratory Techniques in Biochemistry; PCT publicationW095/32291, and Molecular Biology, Elsevier Science Publishers,Amsterdam, The Netherlands (1985), all of which are hereby incorporatedherein by reference.

[0201] The test samples of the present invention include cells, proteinor membrane extracts of cells, or biological fluids such as sputum,blood, serum,, plasma, or urine. The test sample used in theabove-described method will vary based on the assay format, nature ofthe detection method and the tissues, cells or extracts used as thesample to be assayed. Methods for preparing protein extracts or membraneextracts of cells are well known in the art and can be readily beadapted in order to obtain a sample which is compatible with the systemutilized.

[0202] In another embodiment of the present invention, kits are providedwhich contain the necessary reagents to carry out the assays of thepresent invention.

[0203] Specifically, the invention provides a compartmentalized kit toreceive, in close confinement, one or more containers whichcomprises:(a) a first container comprising one of the Dfs, antigens orantibodies of the present invention; and (b) one or more othercontainers comprising one or more of the following: wash reagents,reagents capable of detecting presence of a bound DF, antigen orantibody.

[0204] In detail, a compartmentalized kit includes any kit in whichreagents are contained in separate containers. Such containers includesmall glass containers, plastic containers or strips of plastic orpaper. Such containers allows one to efficiently transfer reagents fromone compartment to another compartment such that the samples andreagents are not cross-contaminated, and the agents or solutions of eachcontainer can be added in a quantitative fashion from one compartment toanother. Such containers will include a container which will accept thetest sample, a container which contains the antibodies used in theassay, containers which contain wash reagents (such as phosphatebuffered saline, Tris-buffers, etc.), and containers which contain thereagents used to detect the bound antibody, antigen or DF.

[0205] Types of detection reagents include labeled nucleic acid probes,labeled secondary antibodies, or in the alternative, if the primaryantibody is labeled, the enzymatic, or antibody binding reagents whichare capable of reacting with the labeled antibody. One skilled in theart will readily recognize that the disclosed Dfs, antigens andantibodies of the present invention can be readily incorporated into oneof the established kit formats which are well known in the art.

[0206] 4. Screening Assay for Binding Agents

[0207] Using the isolated proteins of the present invention, the presentinvention further provides methods of obtaining and identifying agentswhich bind to a protein encoded by one of the ORFs of the presentinvention or to one of the fragments and the Staphylococcus aureusfragment and contigs herein described.

[0208] In general, such methods comprise steps of:

[0209] contacting an agent with an isolated protein encoded by one ofthe ORFs of the present invention, or an isolated fragment of theStaphylococcus aureus genome; and

[0210] determining whether the agent binds to said protein or saidfragment.

[0211] The agents screened in the above assay can be, but are notlimited to, peptides, carbohydrates, vitamin derivatives, or otherpharmaceutical agents. The agents can be selected and screened at randomor rationally selected or designed using protein modeling techniques.

[0212] For random screening, agents such as peptides, carbohydrates,pharmaceutical agents and the like are selected at random and areassayed for their ability to bind to the protein encoded by the ORF ofthe present invention.

[0213] Alternatively, agents may be rationally selected or designed. Asused herein, an agent is said to be “rationally selected or designed”when the agent is chosen based on the configuration of the particularprotein. For example, one skilled in the art can readily adapt currentlyavailable procedures to generate peptides, pharmaceutical agents and thelike capable of binding to a specific peptide sequence in order togenerate rationally designed antipeptide peptides, for example see Hurbyet al., Application of Synthetic Peptides: Antisense Peptides,” InSynthetic Peptides, A User's Guide, W. H. Freeman, NY (1992), pp.289-307, and Kaspczak et al., Biochemistry 28:9230-8 (1989), orpharmaceutical agents, or the like.

[0214] In addition to the foregoing, one class of agents of the presentinvention, as broadly described, can be used to control gene expressionthrough binding to one of the ORFs or EMFs of the present invention. Asdescribed above, such agents can be randomly screened or rationallydesigned/selected. Targeting the ORF or EMF allows a skilled artisan todesign sequence specific or element specific agents, modulating theexpression of either a single ORF or multiple ORFs which rely on thesame EMF for expression control.

[0215] One class of DNA binding agents are agents which contain baseresidues which hybridize or form a triple helix by binding to DNA orRNA. Such agents can be based on the classic phosphodiester, ribonucleicacid backbone, or can be a variety of sulfhydryl or polymericderivatives which have base attachment capacity.

[0216] Agents suitable for use in these methods usually contain 20 to 40bases and are designed to be complementary to a region of the geneinvolved in transcription (triple helix—see Lee et al., Nucl. Acids Res.6:3073 (1979); Cooney et al., Science 241:456 (1988); and Dervan et al.,Science 251: 1360 (1991)) or to the mRNA itself (antisense—Okano, J.Neurochem. 56:560 (1991); Oligodeoxynucleotides as Antisense Inhibitorsof Gene Expression, CRC Press, Boca Raton, Fla. (1988)). Triple helix-formation optimally results in a shut-off of RNA transcription from DNA,while antisense RNA hybridization blocks translation of an mRNA moleculeinto polypeptide. Both techniques have been demonstrated to be effectivein model systems. Information contained in the sequences of the presentinvention can be used to design antisense and triple helix-formingoligonucleotides, and other DNA binding agents.

[0217] 5. Pharmaceutical Compositions and Vaccines

[0218] The present invention further provides pharmaceutical agentswhich can be used to modulate the growth or pathogenicity ofStaphylococcus aureus, or another related organism, in vivo or in vitro.As used herein, a “pharmaceutical agent” is defined as a composition ofmatter which can be formulated using known techniques to provide apharmaceutical compositions. As used herein, the “pharmaceutical agentsof the present invention” refers the pharmaceutical agents which arederived from the proteins encoded by the ORFs of the present inventionor are agents which are identified using the herein described assays.

[0219] As used herein, a pharmaceutical agent is said to “modulate thegrowth or pathogenicity of Staphylococcus aureus or a related organism,in vivo or in vitro,” when the agent reduces the rate of growth, rate ofdivision, or viability of the organism in question. The pharmaceuticalagents of the present invention can modulate the growth or pathogenicityof an organism in many fashions, although an understanding of theunderlying mechanism of action is not needed to practice the use of thepharmaceutical agents of the present invention. Some agents willmodulate the growth or pathogenicity by binding to an important proteinthus blocking the biological activity of the protein, while other agentsmay bind to a component of the outer surface of the organism blockingattachment or rendering the organism more prone to act the bodies natureimmune system. Alternatively, the agent may comprise a protein encodedby one of the ORFs of the present invention and serve as a vaccine. Thedevelopment and use of vaccines derived from membrane associatedpolypeptides are well known in the art. The inventors have identifiedparticularly preferred immunogenic Staphylococcus aureus polypeptidesfor use as vaccines. Such immunogenic polypeptides are described aboveand summarized below.

[0220] As used herein, a “related organism” is a broad term which refersto any organism whose growth or pathogenicity can be modulated by one ofthe pharmaceutical agents of the present invention. In general, such anorganism will contain a homolog of the protein which is the target ofthe pharmaceutical agent or the protein used as a vaccine. As such,related organisms do not need to be bacterial but may be fungal or viralpathogens.

[0221] The pharmaceutical agents and compositions of the presentinvention may be administered in a convenient manner, such as by theoral, topical, intravenous, intraperitoneal, intramuscular,subcutaneous, intranasal or intradermal routes. The pharmaceuticalcompositions are administered in an amount which is effective fortreating and/or prophylaxis of the specific indication. In general, theyare administered in an amount of at least about 1 mg/kg body weight andin most cases they will be administered in an amount not in excess ofabout 1 g/kg body weight per day. In most cases, the dosage is fromabout 0.1 mg/kg to about 10 g/kg body weight daily, taking into accountthe routes of administration, symptoms, etc.

[0222] The agents of the present invention can be used in native form orcan be modified to form a chemical derivative. As used herein, amolecule is said to be a “chemical derivative” of another molecule whenit contains additional chemical moieties not normally a part of themolecule. Such moieties may improve the molecule's solubility,absorption, biological half life, etc. The moieties may alternativelydecrease the toxicity of the molecule, eliminate or attenuate anyundesirable side effect of the molecule, etc. Moieties capable ofmediating such effects are disclosed in, among other sources,REMINGTON'S PHARMACEUTICAL SCIENCES (1980) cited elsewhere herein.

[0223] For example, such moieties may change an immunological characterof the functional derivative, such as affinity for a given antibody.Such changes in immunomodulation activity are measured by theappropriate assay, such as a competitive type immunoassay. Modificationsof such protein properties as redox or thermal stability, biologicalhalf-life, hydrophobicity, susceptibility to proteolytic degradation orthe tendency to aggregate with carriers or into multimers also may beeffected in this way and can be assayed by methods well known to theskilled artisan.

[0224] The therapeutic effects of the agents of the present inventionmay be obtained by providing the agent to a patient by any suitablemeans (e.g., inhalation, intravenously, intramuscularly, subcutaneously,enterally, or parenterally). It is preferred to administer the agent ofthe present invention so as to achieve an effective concentration withinthe blood or tissue in which the growth of the organism is to becontrolled. To achieve an effective blood concentration, the preferredmethod is to administer the agent by injection. The administration maybe by continuous infusion, or by single or multiple injections.

[0225] In providing a patient with one of the agents of the presentinvention, the dosage of the administered agent will vary depending uponsuch factors as the patient's age, weight, height, sex, general medicalcondition, previous medical history, etc. In general, it is desirable toprovide the recipient with a dosage of agent which is in the range offrom about 1 pg/kg to 10 mg/kg (body weight of patient), although alower or higher dosage may be administered. The therapeuticallyeffective dose can be lowered by using combinations of the agents of thepresent invention or another agent.

[0226] As used herein, two or more compounds or agents are said to beadministered “in combination” with each other when either (1) thephysiological effects of each compound, or (2) the serum concentrationsof each compound can be measured at the same time. The composition ofthe present invention can be administered concurrently with, prior to,or following the administration of the other agent.

[0227] The agents of the present invention are intended to be providedto recipient subjects in an amount sufficient to decrease the rate ofgrowth (as defined above) of the target organism.

[0228] The administration of the agent(s) of the invention may be foreither a “prophylactic” or “therapeutic” purpose. When providedprophylactically, the agent(s) are provided in advance of any symptomsindicative of the organisms growth. The prophylactic administration ofthe agent(s) serves to prevent, attenuate, or decrease the rate of onsetof any subsequent infection. When provided therapeutically, the agent(s)are provided at (or shortly after) the onset of an indication ofinfection. The therapeutic administration of the compound(s) serves toattenuate the pathological symptoms of the infection and to increase therate of recovery.

[0229] The agents of the present invention are administered to asubject, such as a mammal, or a patient, in a pharmaceuticallyacceptable form and in a therapeutically effective concentration. Acomposition is said to be “pharmacologically acceptable” if itsadministration can be tolerated by a recipient patient. Such an agent issaid to be administered in a “therapeutically effective amount” if theamount administered is physiologically significant. An agent isphysiologically significant if its presence results in a detectablechange in the physiology of a recipient patient.

[0230] The agents of the present invention can be formulated accordingto known methods to prepare pharmaceutically useful compositions,whereby these materials, or their functional derivatives, are combinedin admixture with a pharmaceutically acceptable carrier vehicle.Suitable vehicles and their formulation, inclusive of other humanproteins, e.g., human serum albumin, are described, for example, inREMINGTON'S PHARMACEUTICAL SCIENCES, 16^(th) Ed., Osol, A., Ed., MackPublishing, Easton Pa. (1980). In order to form a pharmaceuticallyacceptable composition suitable for effective administration, suchcompositions will contain an effective amount of one or more of theagents of the present invention, together with a suitable amount ofcarrier vehicle.

[0231] Additional pharmaceutical methods may be employed to control theduration of action. Control release preparations may be achieved throughthe use of polymers to complex or absorb one or more of the agents ofthe present invention. The controlled delivery may be effectuated by avariety of well known techniques, including formulation withmacromolecules such as, for example, polyesters, polyamino acids,polyvinyl, pyrrolidone, ethylenevinylacetate, methylcellulose,carboxymethylcellulose, or protamine, sulfate, adjusting theconcentration of the macromolecules and the agent in the formulation,and by appropriate use of methods of incorporation, which can bemanipulated to effectuate a desired time course of release. Anotherpossible method to control the duration of action by controlled releasepreparations is to incorporate agents of the present invention intoparticles of a polymeric material such as polyesters, polyamino acids,hydrogels, poly(lactic acid) or ethylene vinylacetate copolymers.Alternatively, instead of incorporating these agents into polymericparticles, it is possible to entrap these materials in microcapsulesprepared, for example, by coacervation techniques or by interfacialpolymerization with, for example, hydroxymethylcellulose orgelatine-microcapsules and poly(methylmethacylate) microcapsules,respectively, or in colloidal drug delivery systems, for example,liposomes, albumin microspheres, microemulsions, nanoparticles, andnanocapsules or in macroemulsions. Such techniques are disclosed inREMINGTON'S PHARMACEUTICAL SCIENCES (1980).

[0232] The invention further provides a pharmaceutical pack or kitcomprising one or more containers filled with one or more of theingredients of the pharmaceutical compositions of the invention.Associated with such container(s) can be a notice in the form prescribedby a governmental agency regulating the manufacture, use or sale ofpharmaceuticals or biological products, which notice reflects approvalby the agency of manufacture, use or sale for human administration.

[0233] In addition, the agents of the present invention may be employedin conjunction with other therapeutic compounds.

[0234] 6. Shot-Gun Approach to Megabase DNA Sequencing

[0235] The present invention further demonstrates that a large sequencecan be sequenced using a random shotgun approach. This procedure,described in detail in the examples that follow, has eliminated the upfront cost of isolating and ordering overlapping or contiguous subclonesprior to the start of the sequencing protocols.

[0236] Certain aspects of the present invention are described in greaterdetail in the examples that follow. The examples are provided by way ofillustration. Other aspects and embodiments of the present invention arecontemplated by the inventors, as will be clear to those of skill in theart from reading the present disclosure.

ILLUSTRATIVE EXAMPLES

[0237] Libraries and Sequencing

[0238] 1. Shotgun Sequencing Probability Analysis

[0239] The overall strategy for a shotgun approach to whole genomesequencing follows from the Lander and Waterman (Landerman and Waterman,Genomics 2: 231 (1988)) application of the equation for the Poissondistribution. According to this treatment, the probability, P₀, that anygiven base in a sequence of size L, in nucleotides, is not sequencedafter a certain amount, n, in nucleotides, of random sequence has beendetermined can be calculated by the equation P₀=e^(−m), where m is L/n,the fold coverage.” For instance, for a genome of 2.8 Mb, m=1 when 2.8Mb of sequence has been randomly generated (1× coverage). At that point,P₀=e⁻¹=0.37. The probability that any given base has not been sequencedis the same as the probability that any region of the whole sequence Lhas not been determined and, therefore, is equivalent to the fraction ofthe whole sequence that has yet to be determined. Thus, at one-foldcoverage, approximately 37% of a polynucleotide of size L, innucleotides has not been sequenced. When 14 Mb of sequence has beengenerated, coverage is 5× for a 0.2.8 Mb and the unsequenced fractiondrops to 0.0067 or 0.67%. 5× coverage of a 2.8 Mb sequence can beattained by sequencing approximately 17,000 random clones from bothinsert ends with an average sequence read length of 410 bp.

[0240] Similarly, the total gap length, G, is determined by the equationG=Le^(−m), and the average gap size, g, follows the equation, g=L/n.Thus, 5× coverage leaves about 240 gaps averaging about 82 bp in size ina sequence of a polynucleotide 2.8 Mb long.

[0241] The treatment above is essentially that of Lander and Waterman,Genomics 2: 231 (1988).

[0242] 2. Random Library Construction

[0243] In order to approximate the random model described above duringactual sequencing, a nearly ideal library of cloned genomic fragments isrequired. The following library construction procedure was developed toachieve this end.

[0244]Staphylococcus aureus DNA was prepared by phenol extraction. Amixture containing 600 ug DNA in 3.3 ml of 300 mM sodium acetate, 10 mMTris-HCl, 1 mM Na-EDTA, 30% glycerol was sonicated for 1 min. at 0° C.in a Branson Model 450 Sonicator at the lowest energy setting using a 3mm probe. The sonicated DNA was ethanol precipitated and redissolved in500 ul TE buffer.

[0245] To create blunt-ends, a 100 ul aliquot of the resuspended DNA wasdigested with 5 units of BAL31 nuclease (New England BioLabs) for 10 minat 30° C. in 200 ul BAL31 buffer. The digested DNA was phenol-extracted,ethanol-precipitated, redissolved in 100 ul TE buffer, and thensize-fractionated by electrophoresis through a 1.0% low meltingtemperature agarose gel. The section containing DNA fragments 1.6-2.0 kbin size was excised from the gel, and the LGT agarose was melted and theresulting solution was extracted with phenol to separate the agarosefrom the DNA. DNA was ethanol precipitated and redissolved in 20 ul ofTE buffer for ligation to vector.

[0246] A two-step ligation procedure was used to produce a plasmidlibrary with 97% inserts, of which >99% were single inserts. The firstligation mixture (50 ul) contained 2 ug of DNA fragments, 2 ug pUC18 DNA(Pharmacia) cut with SmaI and dephosphorylated with bacterial alkalinephosphatase, and 10 units of T4 ligase (GIBCO/BRL) and was incubated at14° C. for 4 hr. The ligation mixture then was phenol extracted andethanol precipitated, and the precipitated DNA was dissolved in 20 ul TEbuffer and electrophoresed on a 1.0% low melting agarose gel. Discretebands in a ladder were visualized by ethidium bromide-staining and UVillumination and identified by size as insert (i), vector (v), v+i,v+2i, v+3i, etc. The portion of the gel containing v+i DNA was excisedand the v+i DNA was recovered and resuspended into 20 ul TE. The v+i DNAthen was blunt-ended by T4 polymerase treatment for 5 min. at 37° C. ina reaction mixture (50 ul) containing the v+i linears, 500 uM each ofthe 4 dNTPs, and 9 units of T4 polymerase (New England BioLabs), underrecommended buffer conditions. After phenol extraction and ethanolprecipitation the repaired v+i linears were dissolved in 20 ul TE. Thefinal ligation to produce circles was carried out in a 50 ul reactioncontaining 5 ul of v+i linears and 5 units of T4 ligase at 14° Covernight. After 10 min. at 70° C. the following day, the reactionmixture was stored at −20° C.

[0247] This two-stage procedure resulted in a molecularly randomcollection of single-insert plasmid recombinants with minimalcontamination from double-insert chimeras (<1%) or free vector (<3%).

[0248] Since deviation from randomness can arise from propagation theDNA in the host, E. coli host cells deficient in all recombination andrestriction functions (A. Greener, Strategies 3 (1):5 (1990)) were usedto prevent rearrangements, deletions, and loss of clones by restriction.Furthermore, transformed cells were plated directly on antibioticdiffusion plates to avoid the usual broth recovery phase which allowsmultiplication and selection of the most rapidly growing cells.

[0249] Plating was carried out as follows. A 100 ul aliquot of EpicurianColi SURE II Supercompetent Cells (Stratagene 200152) was thawed on iceand transferred to a chilled Falcon 2059 tube on ice. A 1.7 ul aliquotof 1.42 M beta-mercaptoethanol was added to the aliquot of cells to afinal concentration of 25 mM. Cells were incubated on ice for 10 min. A1 ul aliquot of the final ligation was added to the cells and incubatedon ice for 30 min. The cells were heat pulsed for 30 sec. at 42° C. andplaced back on ice for 2 min. The outgrowth period in liquid culture waseliminated from this protocol in order to minimize the preferentialgrowth of any given transformed cell. Instead the transformation mixturewas plated directly on a nutrient rich SOB plate containing a 5 mlbottom layer of SOB agar (5% SOB agar: 20 g tryptone, 5 g yeast extract,0.5 g NaCl, 1.5% Difco Agar per liter of media). The 5 ml bottom layeris supplemented with 0.4 ml of 50 mg/ml ampicillin per 100 ml SOB agar.The 15 ml top layer of SOB agar is supplemented with 1 ml X-Gal (2%), 1ml MgCl₂ (1 M), and 1 ml MgSO₄/100 ml SOB agar. The 15 ml top layer waspoured just prior to plating. Our titer was approximately 100colonies/10 ul aliquot of transformation.

[0250] All colonies were picked for template preparation regardless ofsize. Thus, only clones lost due to “poison” DNA or deleterious geneproducts would be deleted from the library, resulting in a slightincrease in gap number over that expected.

[0251] 3. Random DNA Sequencing

[0252] High quality double stranded DNA plasmid templates were preparedusing an alkaline lysis method developed in collaboration with5Prime- - - >3Prime Inc. (Boulder, Co.). Plasmid preparation wasperformed in a 96-well format for all stages of DNA preparation frombacterial growth through final DNA purification. Average templateconcentration was determined by running 25% of the samples on an agarosegel. DNA concentrations were not adjusted.

[0253] Templates were also prepared from a Staphylococcus aureus lambdagenomic library. An unamplified library was constructed in Lambda DASHII vector (Stratagene). Staphylococcus aureus DNA (>100 kb) waspartially digested in a reaction mixture (200 ul) containing 50 ug DNA,1× Sau3AI buffer, 20 units Sau3AI for 6 min. at 23 C. The digested DNAwas phenol-extracted and centrifuges over a 10-40% sucrose gradient.Fractions containing genomic DNA of 15-25 kb were recovered byprecipitation. One ul of fragments was used with 1 ul of DASHII vector(Stratagene) in the recommended ligation reaction. One ul of theligation mixture was used per packaging reaction following therecommended protocol with the Gigapack II XL Packaging Extract Phagewere plated directly without amplification from the packaging mixture(after dilution with 500 ul of recommended SM buffer and chloroformtreatment). Yield was about 2.5×10⁹ pfu/ul.

[0254] An amplified library was prepared from the primary packagingmixture according to the manufacturer's protocol. The amplified libraryis stored frozen in 7% dimethylsulfoxide. The phage titer isapproximately 1×10⁹ pfu/ml.

[0255] Mini-liquid lysates (0.1 ul) are prepared from randomly selectedplaques and template is prepared by long range PCR. Samples are PCRamplified using modified T3 and T7 primers, and Elongase Supermix (LTI).

[0256] Sequencing reactions are carried out on plasmid templates using acombination of two workstations (BIOMEK 1000 and Hamilton Microlab 2200)and the Perkin-Elmer 9600 thermocycler with Applied Biosystems PRISMReady Reaction Dye Primer Cycle Sequencing Kits for the M13 forward(M13-21) and the M13 reverse (M13RP1) primers. Dye terminator sequencingreactions are carried out on the lambda templates on a Perkin-Elmer 9600Thermocycler using the Applied Biosystems Ready Reaction Dye TerminatorCycle Sequencing kits. Modified T7 and T3 primers are used to sequencethe ends of the inserts from the Lambda DASH II library. Sequencingreactions are on a combination of AB 373 DNA Sequencers and ABI 377 DNAsequencers. All of the dye terminator sequencing reactions are analyzedusing the 2×9 hour module on the AB 377. Dye primer reactions areanalyzed on a combination of ABI 373 and ABI 377 DNA sequencers. Theoverall sequencing success rate very approximately is about 85% forM13-21 and M13RP1 sequences and 65% for dye-terminator reactions. Theaverage usable read length is 485 bp for M13-21 sequences, 445bp forM13RP1 sequences, and 375 bp for dye-terminator reactions.

[0257] 4. Protocol for Automated Cycle Sequencing

[0258] The sequencing was carried out using Hamilton Microstation 2200,Perkin Elmer 9600 thermocyclers, ABI 373 and ABI 377 Automated DNASequencers. The Hamilton combines pre-aliquoted templates and reactionmixes consisting of deoxy- and dideoxynucleotides, the thermostable TaqDNA polymerase, fluorescently-labeled sequencing primers, and reactionbuffer. Reaction mixes and templates were combined in the wells of a96-well thermocycling plate and transferred to the Perkin Elmer 9600thermocycler. Thirty consecutive cycles of linear amplification (i.e..,one primer synthesis) steps were performed including denaturation,annealing of primer and template, and extension; i.e., DNA synthesis. Aheated lid with rubber gaskets on the thermocycling plate preventsevaporation without the need for an oil overlay.

[0259] Two sequencing protocols were used: one for dye-labeled primersand a second for dye-labeled dideoxy chain terminators. The shotgunsequencing involves use of four dye-labeled sequencing primers, one foreach of the four terminator nucleotide. Each dye-primer was labeled witha different fluorescent dye, permitting the four individual reactions tobe combined into one lane of the 373 or 377 DNA Sequencer forelectrophoresis, detection, and base-calling. ABI currently suppliespre-mixed reaction mixes in bulk packages containing all the necessarynon-template reagents for sequencing. Sequencing can be done with bothplasmid and PCR- generated templates with both dye-primers anddye-terminators with approximately equal fidelity, although plasmidtemplates generally give longer usable sequences.

[0260] Thirty-two reactions were loaded per ABI 373 Sequencer each dayand 96 samples can be loaded on an ABI 377 per day. Electrophoresis wasrun overnight (ABI 373) or for 2½ hours (ABI 377) following themanufacturer's protocols. Following electrophoresis and fluorescencedetection, the ABI 373 or ABI 377 performs automatic lane tracking andbase-calling. The lane-tracking was confirmed visually. Each sequenceelectropherogram (or fluorescence lane trace) was inspected visually andassessed for quality. Trailing sequences of low quality were removed andthe sequence itself was loaded via software to a Sybase database(archived daily to 8 mm tape). Leading vector polylinker sequence wasremoved automatically by a software program. Average edited lengths ofsequences from the standard ABI 373 or ABI 377 were around 400 bp anddepend mostly on the quality of the template used for the sequencingreaction.

[0261] Imformatics

[0262] 1. Data Management

[0263] A number of information management systems for a large-scalesequencing lab have been developed. (For review see, for instance,Kerlavage et al., Proceedings of the Twenty-Sixth Annual HawaiiInternational Conference on System Sciences, IEEE Computer SocietyPress, Wash. D.C., 585 (1993)) The system used to collect and assemblethe sequence data was developed using the Sybase relational databasemanagement system and was designed to automate data flow whereverpossible and to reduce user error. The database stores and correlatesall information collected during the entire operation from templatepreparation to final analysis of the genome. Because the raw output ofthe ABI 373 Sequencers was based on a Macintosh platform and the datamanagement system chosen was based on a Unix platform, it was necessaryto design and implement a variety of multi- user, client-serverapplications which allow the raw data as well as analysis results toflow seamlessly into the database with a minimum of user effort.

[0264] 2. Assembly

[0265] An assembly engine (TIGR Assembler) developed for the rapid andaccurate assembly of thousands of sequence fragments was employed togenerate contigs. The TIGR assembler simultaneously clusters andassembles fragments of the genome. In order to obtain the speednecessary to assemble more than 10⁴ fragments, the algorithm builds ahash table of 12 bp oligonucleotide subsequences to generate a list ofpotential sequence fragment overlaps. The number of potential overlapsfor each fragment determines which fragments are likely to fall intorepetitive elements. Beginning with a single seed sequence fragment,TIGR Assembler extends the current contig by attempting to add the bestmatching fragment based on oligonucleotide content. The contig andcandidate fragment are aligned using a modified version of theSmith-Waterman algorithm which provides for optimal gapped alignments(Waterman, M. S., Methods in Enzymology 164: 765 (1988)). The contig isextended by the fragment only if strict criteria for the quality of thematch are met. The match criteria include the minimum length of overlap,the maximum length of an unmatched end, and the minimum percentagematch. These criteria are automatically lowered by the algorithm inregions of minimal coverage and raised in regions with a possiblerepetitive element. The number of potential overlaps for each fragmentdetermines which fragments are likely to fall into repetitive elements.Fragments representing the boundaries of repetitive elements andpotentially chimeric fragments are often rejected based on partialmismatches at the ends of alignments and excluded from the currentcontig. TIGR Assembler is designed to take advantage of clone sizeinformation coupled with sequencing from both ends of each template. Itenforces the constraint that sequence fragments from two ends of thesame template point toward one another in the contig and are locatedwithin a certain ranged of base pairs (definable for each clone based onthe known clone size range for a given library).

[0266] 3. Identifying Genes

[0267] Tables 1, 2, and 3 list ORFs in the Staphylococcus aureus genomiccontigs of the present invention that were identified as putative codingregions by the GeneMark software using organism-specific second-orderMarkov probability transition matrices. It will be appreciated thatother criteria can be used, in accordance with well known analyticalmethods, such as those discussed herein, to generate more inclusive,more restrictive, or more selective lists.

[0268] Table 1 sets out ORFs in the Staphylococcus aureus contigs of thepresent invention that over a continuous region of at least 50 bases are95% or more identical (by BLASTN analysis) to a nucleotide sequenceavailable through Genbank in November 1996.

[0269] Table 2 sets out ORFs in the Staphylococcus aureus contigs of thepresent invention that are not in Table 1 and match, with a BLASTPprobability score of 0.01 or less, polypeptide sequence availablethrough a non-redundant database of known protein generated by combiningthe Swiss-Prot, PIR, and GenPept databases.

[0270] Table 3 sets out the remaining ORFs in the Staphylococcus aureuscontigs of the present invention, which did not have significant matchesto the public databases by the criteria described above.

[0271] Illustrative Applications

[0272] 1. Production of an Antibody to a Staphylococcus aureus Protein

[0273] Substantially pure protein or polypeptide is isolated from thetransfected or transformed cells using any one of the methods known inthe art. The protein can also be produced in a recombinant prokaryoticexpression system, such as E. coli, or can by chemically synthesized.Concentration of protein in the final preparation is adjusted, forexample, by concentration on an Amicon filter device, to the level of afew micrograms/ml. Monoclonal or polyclonal antibody to the protein canthen be prepared as follows.

[0274] 2. Monoclonal Antibody Production by Hybridoma Fusion

[0275] Monoclonal antibody to epitopes of any of the peptides identifiedand isolated as described can be prepared from murine hybridomasaccording to the classical method of Kohler, G. and Milstein, C., Nature256:495 (1975) or modifications of the methods thereof. Briefly, a mouseis repetitively inoculated with a few micrograms of the selected proteinover a period of a few weeks. The mouse is then sacrificed, and theantibody producing cells of the spleen isolated. The spleen cells arefused by means of polyethylene glycol with mouse myeloma cells, and theexcess unfused cells destroyed by growth of the system on selectivemedia comprising aminopterin (HAT media). The successfully fused cellsare diluted and aliquots of the dilution placed in wells of a microtiterplate where growth of the culture is continued. Antibody-producingclones are identified by detection of antibody in the supernatant fluidof the wells by immunoassay procedures, such as ELISA, as originallydescribed by Engvall, E., Meth. Enzymol. 70:419 (1980), and modifiedmethods thereof. Selected positive clones can be expanded and theirmonoclonal antibody product harvested for use. Detailed procedures formonoclonal antibody production are described in Davis, L. et al. BasicMethods in Molecular Biology Elsevier, New York. Section 21-2 (1989).

[0276] 3. Polyclonal Antibody Production by Immunization

[0277] Polyclonal antiserum containing antibodies to heterogenousepitopes of a single protein can be prepared by immunizing suitableanimals with the expressed protein described above, which can beunmodified or modified to enhance immunogenicity. Effective polyclonalantibody production is affected by many factors related both to theantigen and the host species. For example, small molecules tend to beless immunogenic than other and may require the use of carriers andadjuvant. Also, host animals vary in response to site of inoculationsand dose, with both inadequate or excessive doses of antigen resultingin low titer antisera. SmaII doses (ng level) of antigen administered atmultiple intradermal sites appears to be most reliable. An effectiveimmunization protocol for rabbits can be found in Vaitukaitis, J. etal., J. Clin. Endocrinol. Metab. 33:988-991 (1971).

[0278] Booster injections can be given at regular intervals, andantiserum harvested when antibody titer thereof, as determinedsemi-quantitatively, for example, by double immunodiffusion in agaragainst known concentrations of the antigen, begins to fall. See, forexample, Ouchterlony, O. et al, Chap. 19 in: Handbook of ExperimentalImmunology, Wier, D., ed, Blackwell (1973). Plateau concentration ofantibody is usually in the range of 0.1 to 0. 2 mg/ml of serum (about12M). Affinity of the antisera for the antigen is determined bypreparing competitive binding curves, as described, for example, byFisher, D., Chap. 42 in: Manual of Clinical Immunology, second edition,Rose and Friedman, eds., Amer. Soc. For Microbiology, Wash., D.C. (1980)

[0279] Antibody preparations prepared according to either protocol areuseful in quantitative immunoassays which determine concentrations ofantigen-bearing substances in biological samples; they are also usedsemi-quantitatively or qualitatively to identify the presence of antigenin a biological sample. In addition, they are useful in various animalmodels of Staphylococcal disease known to those of skill in the art as ameans of evaluating the protein used to make the antibody as a potentialvaccine target or as a means of evaluating the antibody as a potentialimmunothereapeutic reagent.

[0280] 4. Preparation of PCR Primers and Amplification of DNA

[0281] Various fragments of the Staphylococcus aureus genome, such asthose of Tables 1-3 and SEQ ID NOS: 1-5,191 can be used, in accordancewith the present invention, to prepare PCR primers for a variety ofuses. The PCR primers are preferably at least 15 bases, and morepreferably at least 18 bases in length. When selecting a primersequence, it is preferred that the primer pairs have approximately thesame G/C ratio, so that melting temperatures are approximately the same.The PCR primers and amplified DNA of this Example find use in theExamples that follow.

[0282] 5. Gene Expression from DNA Sequences Corresponding to ORFs

[0283] A fragment of the Staphylococcus aureus genome provided in Tables1-3 is introduced into an expression vector using conventionaltechnology. Techniques to transfer cloned sequences into expressionvectors that direct protein translation in mammalian, yeast, insect orbacterial expression systems are well known in the art. Commerciallyavailable vectors and expression systems are available from a variety ofsuppliers including Stratagene (La Jolla, Calif.), Promega (Madison,Wis.), and Invitrogen (San Diego, Calif.). If desired, to enhanceexpression and facilitate proper protein folding, the codon context andcodon pairing of the sequence may be optimized for the particularexpression organism, as explained by Hatfield et al., U.S. Pat. No.5,082,767, incorporated herein by this reference.

[0284] The following is provided as one exemplary method to generatepolypeptide(s) from cloned ORFs of the Staphylococcus aureus genomefragment. Bacterial ORFs generally lack a poly A addition signal. Theaddition signal sequence can be added to the construct by, for example,splicing out the poly A addition sequence from pSG5 (Stratagene) usingBglI and SalI restriction endonuclease enzymes and incorporating it intothe mammalian expression vector pXT1 (Stratagene) for use in eukaryoticexpression systems. pXT1 contains the LTRs and a portion of the gag geneof Moloney Murine Leukemia Virus. The positions of the LTRs in theconstruct allow efficient stable transfection. The vector includes theHerpes Simplex thymidine kinase promoter and the selectable neomycingene. The Staphylococcus aureus DNA is obtained by PCR from thebacterial vector using oligonucleotide primers complementary to theStaphylococcus aureus DNA and containing restriction endonucleasesequences for PstI incorporated into the 5′ primer and BglII at the 5′end of the corresponding Staphylococcus aureus DNA 3′ primer, takingcare to ensure that the Staphylococcus aureus DNA is positioned suchthat its followed with the poly A addition sequence. The purifiedfragment obtained from the resulting PCR reaction is digested with PstI,blunt ended with an exonuclease, digested with BglII, purified andligated to pXT1, now containing a poly A addition sequence and digestedBglII.

[0285] The ligated product is transfected into mouse NIH 3T3 cells usingLipofectin (Life Technologies, Inc., Grand Island, N.Y.) underconditions outlined in the product specification. Positive transfectantsare selected after growing the transfected cells in 600 ug/ml G418(Sigma, St. Louis, Mo.). The protein is preferably released into thesupernatant. However if the protein has membrane binding domains, theprotein may additionally be retained within the cell or expression maybe restricted to the cell surface. Since it may be necessary to purifyand locate the transfected product, synthetic 15-mer peptidessynthesized from the predicted Staphylococcus aureus DNA sequence areinjected into mice to generate antibody to the polypeptide encoded bythe Staphylococcus aureus DNA.

[0286] Alternatively and if antibody production is not possible, theStaphylococcus aureus DNA sequence is additionally incorporated intoeukaryotic expression vectors and expressed as, for example, a globinfusion. Antibody to the globin moiety then is used to purify thechimeric protein. Corresponding protease cleavage sites are engineeredbetween the globin moiety and the polypeptide encoded by theStaphylococcus aureus DNA so that the latter may be freed from theformed by simple protease digestion. One useful expression vector forgenerating globin chimerics is pSG5 (Stratagene). This vector encodes arabbit globin. Intron II of the rabbit globin gene facilitates splicingof the expressed transcript, and the polyadenylation signal incorporatedinto the construct increases the level of expression. These techniquesare well known to those skilled in the art of molecular biology.Standard methods are published in methods texts such as Davis et al.,cited elsewhere herein, and many of the methods are available from thetechnical assistance representatives from Stratagene, Life Technologies,Inc., or Promega. Polypeptides of the invention also may be producedusing in vitro translation systems such as in vitro Express™ TranslationKit (Stratagene).

[0287] While the present invention has been described in some detail forpurposes of clarity and understanding, one skilled in the art willappreciate that various changes in form and detail can be made withoutdeparting from the true scope of the invention.

[0288] All patents, patent applications and publications referred toabove are hereby incorporated by reference. TABLE 1 S. aureus - Codingregions containing known sequences HSP ORF Contig ID ORF ID Start (nt)Stop (nt) match acession match gene name percent ident nt length ntlength 1 1 757 95 emb|X17301|SAHD S. aureus DNA for hld gene and forpart of agr gene 100 663 663 1 2 2452 1631 emb|X52543|SAAG S. aureusagrA, agrB and hld genes 99 809 822 1 5 5651 4884 dbj|D14711|STAHStaphylococcus aureus HSP10 and HSP60 genes 98 223 768 5 1 439 71emb|X72700|SAPV S. aureus genes for S and F components ofPanton-Valentine leucocidins 81 216 369 5 4 3571 2111 emb|X72700|SAPV S.aureus genes for S and F components of Panton-Valentine leucocidins 95424 1461 10 1 86 904 gb|L25288| Staphylococcus aureus gyrase-likeprotein alpha and beta subunit (grlA and 98 715 819 grlB) genes,complete cds 16 5 5302 6246 gb|U35773| Staphylococcus aureusprolipoprotein diacylglyceryl transferase (lgt) gene, complete cds 94251 945 16 6 6249 7091 gb|U35773| Staphylococcus aureus prolipoproteindiacylglyceryl transferase (lgt) gene, 99 843 843 complete cds 16 7 70847584 gb|U35773| Staphylococcus aureus prolipoprotein diacylglyceryltransferase (lgt) gene, 99 342 501 complete cds 20 1 549 103 gb|L19300|Staphylococcus aureus DNA sequence encoding three ORFs, complete cds;prophage phi-11 100 443 447 sequence homology, 5′ flank 20 2 841 671gb|L19300| Staphylococcus aureus DNA sequence encoding three ORFs,complete cds; prophage phi-11 91 137 171 sequence homology, 5′ flank 203 1798 1586 gb|L19300| Staphylococcus aureus DNA sequence encoding threeORFs, complete cds; prophage phi-11 100 110 213 sequence homology, 5′flank 20 4 3825 2350 gb|M76714| Staphylococcus aureus peptidoglycanhydrolase gene, complete cds 100 948 1476 20 5 4282 3776 gb|M76714|Staphylococcus aureus peptidoglycan hydrolase gene, complete cds 100 309507 26 1 2 145 gb|U41072| Staphylococcus aureus isoleucyl-tRNAsynthetase (ileS) gene, partial cds 100 126 144 26 2 84 557 gb|U41072|Staphylococcus aureus isoleucyl-tRNA synthetase (ileS) gene, partial cds99 430 474 26 3 763 3531 emb|X74219|SAIL S. aureus gene forisoleucyl-tRNA synthetase 99 2769 2769 29 3 1261 4392 gb|U66665|Staphylococcus aureus DNA fragment with class II promoter activity 100117 3132 31 14 13463 11949 emb|X73889|SAP1 S. aureus genes P1 and P2 991351 1515 31 15 13855 13469 emb|X73889|SAP1 S. aureus genes P1 and P2 98258 387 38 17 13112 11940 gb|M12715| S. aureus geh gene encoding lipase(glycerol ester hydrolase) 100 372 1173 38 19 13434 15518 gb|M12715| S.aureus geh gene encoding lipase (glycerol ester hydrolase) 100 2085 208546 2 519 1727 gb|U73374| Staphylococcus aureus type 8 capsule genes,cap8A, cap8B, cap8C, cap8D, cap8E, cap8F, cap8G, 98 1209 1209 cap8H,cap8I, cap8J, cap8K, cap8L, cap8M, cap8N, cap8O, cap8P, complete cds 463 1720 2295 gb|U73374| Staphylococcus aureus type 8 capsule genes,cap8A, cap8B, cap8C, cap8D, cap8E, cap8F, cap8G, 98 576 576 cap8H,cap8I, cap8J, cap8K, cap8L, cap8M, cap8N, cap8O, cap8P, complete cds 464 2259 3182 gb|U73374| Staphylococcus aureus type 8 capsule genes,cap8A, cap8B, cap8C, cap8D, cap8E, cap8F, cap8G, 97 924 924 cap8H,cap8I, cap8J, cap8K, cap8L, cap8M, cap8N, cap8O, cap8P, complete cds 465 3173 4498 gb|U73374| Staphylococcus aureus type 8 capsule genes,cap8A, cap8B, cap8C, cap8D, cap8E, cap8F, cap8G, 98 1283 1326 cap8H,cap8I, cap8J, cap8K, cap8L, cap8M, cap8N, cap8O, cap8P, complete cds 466 4536 5720 gb|U73374| Staphylococcus aureus type 8 capsule genes,cap8A, cap8B, cap8C, cap8D, cap8E, cap8F, cap8G, 98 1185 1185 cap8H,cap8I, cap8J, cap8K, cap8L, cap8M, cap8N, cap8O, cap8P, complete cds 467 6120 5785 gb|U73374| Staphylococcus aureus type 8 capsule genes,cap8A, cap8B, cap8C, cap8D, cap8E, cap8F, cap8G, 99 278 336 cap8H,cap8I, cap8J, cap8K, cap8L, cap8M, cap8N, cap8O, cap8P, complete cds 481 2 955 gb|L25893| Staphylococcus aureus recA gene, complete cds 99 954954 50 3 2924 1383 emb|X85029|SAAH S. aureus AhpC gene 100 88 1542 50 43515 2922 emb|X85029|SAAH S. aureus AhpC gene 98 540 594 54 3 3392 1710emb|X62992|SAFN S. aureus fnbB gene for fibronectin binding protein B100 1668 1683 54 4 4122 3379 emb|X62992|SAFN S. aureus fnbB gene forfibronectin binding protein B 99 720 744 54 5 4562 4068 emb|X62992|SAFNS. aureus fnbB gene for fibronectin binding protein B 100 463 495 54 68300 5214 gb|J04151| S. aureus fibronectin-binding protein (fnbA) mRNA,complete cds 100 3087 3087 58 3 1743 2819 emb|X87104|SADN S. aureus mdr,pbp4 and taqD genes (SG511-55 isolate) 89 68 1077 58 4 2858 3280emb|X91786|SAPB S. aureus abcA, pbp4, and tagD genes 99 423 423 58 54701 3397 emb|X91786|SAPB S. aureus abcA, pbp4, and tagD genes 99 13051305 58 6 5378 5079 gb|U29478| Staphylococcus aureus ABCtransporter-like protein AbcA (abcA) gene, 100 300 300 partial cds 58 75086 6840 emb|X91786|SAPB S. aureus abcA, pbp4, and tagD genes 99 17551755 72 1 445 2 gb|M21854| S. aureus agr gene encoding an accessory generegulator protein, complete 100 444 444 cds 72 2 1453 449emb|X52543|SAAG S. aureus agrA, agrB and hld genes 99 673 1005 82 1 3573917 emb|X64172|SARP S. aureus rp1L, orf202, rpoB(rif) and rpoC genesfor ribosomal protein 99 2396 3561 L7/L12, hypothetical protein ORF202,DNA-directed RNA polymerase beta & beta’ chains 82 2 4027 7677emb|X89233|SARP S. aureus DNA for rpoC gene 99 3171 3651 82 3 7745 8068gb|U20869| Staphylococcus aureus ribosomal protein S12 (rpsL) gene,complete cds, 100 320 324 ribosomal protein S7 (rpsG) and ORF 1 genes,partial cds 82 4 8103 8579 gb|U20869| Staphylococcus aureus ribosomalprotein S12 (rpsL) gene, complete cds, 100 477 477 ribosomal protein S7(rpsG) and ORF 1 genes, partial cds 82 5 8618 8821 gb|U20869|Staphylococcus aureus ribosomal protein S12 (rpsL) gene, complete cds,100 154 204 ribosomal protein S7 (rpsG) and ORF 1 genes, partial cds 841 18 191 gb|U73374| Staphylococcus aureus type 8 capsule genes, cap8A,cap8B, cap8C, cap8D, cap8E, cap8F, cap8G, 98 164 174 cap8H, cap8I,cap8J, cap8K, cap8L, cap8M, cap8N, cap8O, cap8P, complete cds 84 2 189893 gb|U73374| Staphylococcus aureus type 8 capsule genes, cap8A, cap8B,cap8C, cap8D, cap8E, cap8F, cap8G, 94 705 705 cap8H, cap8I, cap8J,cap8K, cap8L, cap8M, cap8N, cap8O, cap8P, complete cds 84 3 887 1660gb|U73374| Staphylococcus aureus type 8 capsule genes, cap8A, cap8B,cap8C, cap8D, cap8E, cap8F, cap8G, 99 774 774 cap8I, cap8J, cap8K,cap8L, cap8M, cap8N, cap8O, cap8P, complete cds 84 4 1584 3503gb|U73374| Staphylococcus aureus type 8 capsule genes, cap8A, cap8B,cap8C, cap8D, cap8E, cap8F, cap8G, 98 1920 1920 cap8H, cap8I, cap8J,cap8K, cap8L, cap8M, cap8N, cap8O, cap8P, complete cds 84 5 3394 4521gb|U73374| Staphylococcus aureus type 8 capsule genes, cap8A, cap8B,cap8C, cap8D, cap8E, cap8F, cap8G, 97 1128 1128 cap8H, cap8I, cap8J,cap8K, cap8L, cap8M, cap8N, cap8O, cap8P, complete cds 84 6 4519 5643gb|U73374| Staphylococcus aureus type 8 capsule genes, cap8A, cap8B,cap8C, cap8D, cap8E, cap8F, cap8G, 97 1125 1125 cap8H, cap8I, cap8J,cap8K, cap8L, cap8M, cap8N, cap8O, cap8P, complete cds 96 2 1245 3896emb|Z18852|SACF S. aureus gene for clumping factor 83 660 2652 97 2 625882 gb|U41072| Staphylococcus aureus isoleucyl-tRNA synthetase (ileS)gene, partial cds 97 68 258 111 1 3 452 gb|L41499| Staphylococcus aureusORF1, partial cds, ORF2, ORF3, autolysin (atl) genes, 100 450 450complete cds 111 2 526 1041 gb|L41499| Staphylococcus aureus ORF1,partial cds, ORF2, ORF3, autolysin (atl) genes, 99 516 516 complete cds117 2 1278 1958 gb|M83994| Staphylococcus aureus prolipoprotein signalpeptidase (lsp) gene, complete 100 61 681 cds 118 4 3787 4254dbj|D30690|STAN Staphylococcus aureus genes for ORF37; HSP20; HSP70;HSP40; ORF35, complete 99 467 468 cds 130 4 2597 3640 emb|X13290|SATNStaphylococcus aureus multi-resistance plasmid pSK1 DNA containing 78956 1044 transposon Tn4003 130 5 3813 4265 emb|z16422|SADI S. aureusdfrB gene for dihydrofolate reductase 98 416 453 130 6 4309 5172emb|z16422|SADI S. aureus dfrB gene for dihydrofolate reductase 98 607864 136 4 5296 6207 emb|X71437|SAGY S. aureus genes gyrB, gyrA and recF(partial) 97 838 912 136 5 8987 6294 dbj|D10489|STAG Staphylococcusaureus genes for DNA gyrase A and B, complete cds 100 2694 2694 136 610940 8994 dbj|D10489|STAG Staphylococcus aureus genes for DNA gyrase Aand B, complete cds 99 1947 1947 136 7 11765 10938 gb|S77055| recFcluster: dnaA = replisome assembly protein...gyrB = DNA gyrase beta 99822 828 subunit [Staphylococcus aureus, YB886, Genomic, 5 genes, 3573nt] 143 3 2867 1563 gb|U36379| Staphylococcus aureusS-adenosylmethionine synthetase gene, complete cds 99 1305 1305 143 43100 4281 gb|L42943| Staphylococcus aureus (clone KIN50)phosphoenolpyruvate carboxykinase 100 1170 1182 (pckA) gene, completecds 143 5 4254 4718 gb|U51133| Staphylococcus aureus phosphoenolpyruvatecarboxykinase (pcka) gene, 100 449 465 complete cds 143 9 6977 7261gb|U51132| Staphylococcus aureus o-succinylbenzoic acid CoA ligase(mene), and o- 100 75 285 succinylbenzoic acid synthetase (menc) genes,complete cds 143 10 8361 7258 gb|U51132| Staphylococcus aureuso-succinylbenzoic acid CoA ligase (mene), and o- 100 1104 1104succinylbenzoic acid synthetase (menc) genes, complete cds 143 11 97488264 gb|U51132| Staphylococcus aureus o-succinylbenzoic acid CoA ligase(mene), and o- 100 1485 1485 succinylbenzoic acid synthetase (menc)genes, complete cds 143 12 10320 9901 gb|U51132| Staphylococcus aureuso-succinylbenzoic acid CoA ligase (mene), and o- 100 332 420succinylbenzoic acid synthetase (mene) genes, complete cds 152 5 24543437 emb|X58434|SAPD S. aureus pdhB, pdhC and pdhD genes for pyruvatedecarboxylase, 99 305 984 dihydrolipoamide acetyltransferase anddihydrolipoamide dehydrogenase 152 6 3513 4820 emb|X58434|SAPD S. aureuspdhB, pdhC and pdhD genes for pyruvate decarboxylase, 98 1308 1308dihydrolipoamide acetyltransferase and dihydrolipoamide dehydrogenase152 7 4818 6230 emb|X58434|SAPD S. aureus pdhB, pdhC and pdhD genes forpyruvate decarboxylase, 99 1413 1413 dihydrolipoamide acetyltransferaseand dihydrolipoamide dehydrogenase 153 1 387 1526 gb|S77055| recFcluster: dnaA = replisome assembly protein.. .gyrB = DNA gyrase beta 991140 1140 subunit [Staphylococcus aureus, YB886, Genomic, 5 genes, 3573nt] 153 2 1877 2152 gb|S77055| recF cluster: dnaA = replisome assemblyprotein...gyrB = DNA gyrase beta 100 276 276 subunit [Staphylococcusaureus, YB886, Genomic, 5 genes, 3573 nt] 153 3 2143 2289 gb|S77055|recF cluster; dnaA = replisome assembly protein...gyrB = DNA gyrase beta99 113 147 subunit [Staphylococcus aureus, YB886, Genomic, 5 genes, 3573nt] 154 10 9314 7836 gb|U06451| Staphylococcus aureus proline permeasehomolog (putP) gene, complete cds 91 154 1479 154 11 9615 9295gb|U06451| Staphylococcus aureus proline permease homolog (putP) gene,complete cds 99 229 321 154 12 9943 10167 gb|U06451| Staphylococcusaureus proline permease homolog (putP) gene, complete cds 94 123 225 15413 10089 11501 gb|U06451| Staphylococcus aureus proline permease homolog(putP) gene, complete cds 99 1326 1413 159 2 1212 229 dbj|D28879|STAPStaphylococcus aureus gene for penicillin-binding protein 1, completecds 100 71 984 161 3 2270 1944 gb|M83994| Staphylococcus aureusprolipoprotein signal peptidase (lsp) gene, complete 92 203 327 cds 1621 705 4 gb|U21221| Staphylococcus aureus hyaluronate lyase (hysA) gene,complete cds 100 702 702 163 4 1263 1772 gb|U19770| Staphylococcusaureus pyrrolidone carboxyl peptidase (pcp) gene, complete 96 127 510cds 164 7 4774 9117 dbj|D86727|D867 Staphylococcus aureus DNA for DNApolymerase III, complete cds 99 3470 4344 168 7 6447 5446 gb|U21636|Staphylococcus aureus cmp-binding-factor 1 (cbf1) and ORF X genes,complete 100 1002 1002 cds 168 8 7961 6384 gb|U21636| Staphylococcusaureus cmp-binding-factor 1 (cbf1) and ORF X genes, complete 99 11581578 cds 173 6 7801 6362 gb|J03479| S. aureus enzyme III-lac (lacF),enzyme II-lac (lacE), and phospho-beta- 100 1440 1440 galactosidase(lacG) genes, complete cds 173 7 9522 7792 gb|J03479| S. aureus enzymeIII-lac (lacF), enzyme II-lac (lacE), and phospho-beta- 99 1731 1731galactosidase (lacG) genes, complete cds 173 8 8285 8704 gb|J03479| S.aureus enzyme III-lac (lacF), enzyme II-lac (lacE), and phospho-beta-100 420 420 galactosidase (lacG) genes, complete cds 173 9 9839 9510gb|J03479| S. aureus enzyme III-lac (lacF), enzyme II-lac (lacE), andphospho-beta- 100 330 330 galactosidase (lacG) genes, complete cds 17310 10829 9843 emb|X14827|SALA Staphylococcus aureus lacC and lacD genes100 987 987 173 11 11774 10827 emb|X14827|SALA Staphylococcus aureuslacC and lacD genes 100 948 948 173 12 12305 11772 gb|M64724| S. aureustagatose 6-phosphate isomerase gene, complete cds 100 534 534 173 1312773 12303 gb|M32103| Staphylococcus aureus lac repressor (lacR) gene,complete cds and lacA 100 471 471 repressor (lacA), partial cds 173 1413866 13099 gb|M32103| Staphylococcus aureus lac repressor (lacR) gene,complete cds and lacA 100 768 768 repressor (lacA), partial cds 178 1 2655 gb|U52961| Staphylococcus aureus holin-like protein LrgA (lrgA) andLrgB (lrgB) genes, 100 115 654 complete cds 178 2 1482 763 gh|U52961|Staphylococcus aureus holin-like protein LrgA (lrgA) and LrgB (lrgB)genes, 100 720 720 complete cds 178 3 1909 1457 gb|U52961|Staphylococcus aureus holin-like protein LrgA (lrgA) and LrgB (lrgB)genes, 100 453 453 complete cds 178 4 1551 1853 gb|U52961|Staphylococcus aureus holin-like protein LrgA (lrgA) and LrgB (lrgB)genes, 100 303 303 complete cds 178 5 2777 2013 gb|L42945|Staphylococcus aureus lytS and lytR genes, complete cds 99 765 765 178 63025 2756 gb|L42945| Staphylococcus aureus lytS and lytR genes, completecds 99 270 270 181 1 590 66 gb|M63177| S. aureus sigma factor (plaC)gene, complete cds 99 499 525 182 1 3 341 emb|X61307|SASP Staphylococcusaureus spa gene for protein A 98 277 339 182 2 690 2312 gb|J01786| S.aureus spa gene coding for protein A, complete csd 97 1332 1623 182 34251 2641 emb|X61307|SASP Staphylococcus aureus spa gene for protein A99 119 1611 185 1 3 824 gb|U31979| Staphylococcus aureus chorismatesynthase (aroC) and nucleoside diphosphate 90 132 822 kinase (ndk)genes, complete cds, dehydroauinate synthase (aroB) and geranylgeranylpyrophosphate synthetase homolog (gerCC) genes, partial cds 191 3 8412760 emb|X17679|SACO Staphylococcus aureus coa gene for coagulase 991920 1920 191 4 2967 3143 emb|X16457|SAST Staphylococcus aureus gene forstaphylocoagulase 99 177 177 191 5 4566 3364 emb|X16457|SASTStaphylococcus aureus gene for staphylocoagulase 99 250 1203 196 1 872 3gb|L36472| Staphylococcus aureus lysyl-tRNA sythetase gene, completecds, transfer RNA 99 870 870 (tRNA) genes, 5S ribosomal RNA (5S rRNA)gene, 16S ribosomal RNA (16S rRNA) gene, 23S ribosomal RNA (23S rRNA)gene 198 3 1688 2011 emb|X93205|SAPT S. aureus ptsH and ptsI genes 99324 324 198 4 2005 2310 emb|X93205|SAPT S. aureus ptsH and ptsI genes 97304 306 202 1 163 1305 emb|X97985|SA12 S. aureus orfs 1,2,3 & 4 99 11431143 202 2 1303 2175 emb|X73889|SAP1 S. aureus genes P1 and P2 94 444873 210 1 1558 2 dbj|D17366|STAA Staphylococcus aureus atl gene forautolysin, complete cds and other ORFs 99 1552 1557 210 2 2232 1525gb|L41499| Staphylococcus aureus ORF1, partial cds, ORF2, ORF3,autolysin (atl) genes, 99 684 708 complete cds 214 11 7429 7770dbj|D86240|D862 Staphylococcus aureus gene for unkown function and dltoperon dltA, dltB, 96 157 342 dltC and dltD genes, complete cds 216 3398 1318 emb|X72700|SAPV S. aureus genes for S and F components ofPanton-Valentine leucocidins 88 265 921 219 2 1073 336 dbj|D30690|STANStaphylococcus aureus genes for ORF37; HSP20; HSP70; HSP40; ORF35,complete 100 60 738 cds 219 3 2035 1091 dbj|D30690|STAN Staphylococcusaureus genes for ORF37; HSP20; HSP70; HSP40; ORF35, complete 99 945 945cds 219 4 3196 2033 dbj|D30690|STAN Staphylococcus aureus genes forORF37; HSP20; HSP70; HSP40; ORF35, complete 99 1164 1164 cds 219 5 51763308 dbj|D30690|STAN Staphylococcus aureus genes for ORF37; HSP20;HSP70; HSP40; ORF35, complete 98 1869 1869 cds 219 6 5883 5209dbj|D30690|STAN Staphylococcus aureus genes for ORF37; HSP20; HSP70;HSP40, ORF35, complete 99 675 675 cds 219 7 6334 5867 dbj|D30690|STANStaphylococcus aureus genes for ORF37; HSP20; HSP70; HSP40; ORF35,complete 98 468 468 cds 221 8 10034 9252 gb|L19298| Staphylococcusaureus phosphatidylinositol-specific phospholipase C (plc) 91 67 783gene, complete cds 223 1 1506 157 gb|U73374| Staphylococcus aureus type8 capsule genes, cap8A, cap8B, cap8C, cap8D, 99 102 1350 cap8E, cap8F,cap8G, cap8H, cap8I, cap8J, cap8K, cap8L, cap8M, cap8N, cap8O, cap8P,complete cds 234 1 2 1357 emb|X97985|SA12 S. aureus orfs 1,2,3 & 4 100176 1356 234 2 1694 2485 emb|X97985|SA12 S. aureus orfs 1,2,3 & 4 100792 792 234 3 2648 3148 emb|X97985|SA12 S. aureus orfs 1,2,3 & 4 99 501501 234 4 3120 4604 emb|X97985|SA12 S. aureus orfs 1,2,3 & 4 99 13051485 236 6 3826 5322 gb|U48826| Staphylococcus aureus elastin bindingprotein (ebpS) gene, complete cds 96 648 1497 248 1 2 403emb|X62288|SAPE S. aureus DNA for penicillin-binding protein 2 100 103402 248 2 388 852 gb|L25426| Staphylococcus aureus penicillin-bindingprotein 2 (pbp2) gene, complete 99 465 465 cds 253 2 1093 647 gb|U46541|Staphylococcus aureus sarA gene, complete cds 96 447 447 254 2 150 1835gb|U57060| Staphylococcus aureus scdA gene, complete cds 94 142 1686 2543 1973 2728 gb|U57060| Staphylococcus aureus scdA gene, complete cds 99756 756 260 1 2 1900 gb|M90693| Staphylococcus aureus glycerol esterhydrolase (lip) gene, complete cds 99 1213 1899 265 1 1 942dbj|D21131|STAS Staphylococcus aureus gene for a participant inhomogeneous expression of 99 941 942 high-level methicillin resistance,complete cds 265 2 476 264 dbj|D21131|STAS Staphylococcus aureus genefor a participant in homogeneous expression of 99 213 213 high-levelmethicillin resistance, complete cds 265 3 1765 1112 dbj|D21131|STASStaphylococcus aureus gene for a participant in homogeneous expressionof 98 69 654 high-level methicillin resistance, complete cds 266 1 21018 dbj|D14711|STAH Staphylococcus aureus HSP10 and HSP60 genes 98 7431017 282 1 1 525 gb|S72488| hemB = porphobilinogen synthase[Staphylococcus aureus, SA1959, Genomic, 1087 100 110 525 nt] 282 2 5161502 gb|S72488| hemB = porphobilinogen synthase [Staphylococcus aureus,SA1959, Genomic, 1087 100 952 987 nt] 284 1 3 170 gb|M63176|Staphylococcus aureus helicase required for T181 replication (pcrA)gene, 98 84 168 complete cds 284 2 282 1034 gb|M63176| Staphylococcusaureus helicase required for T181 replication (pcrA) gene, 100 712 753complete cds 284 3 1028 2026 gb|M63176| Staphylococcus aureus helicaserequired for T181 replication (pcrA) gene, 99 979 999 complete cds 284 41990 2202 gb|M63176| Staphylococcus aureus helicase required for T181replication (pcrA) gene, 98 187 213 complete cds 289 3 1536 1991gb|M32470| S. aureus Sau3AI-restriction-enzyme andSau3AI-modification-enzyme genes, 99 338 456 complete cds 303 1 2 868gb|L01055| Staphylococcus aureus gamma-hemolysin components A, B and C(hlgA, hlgB, 99 867 867 hglC) genes, complete cds 303 2 1409 2383gb|L01055| Staphylococcus aureus gamma-hemolysin components A, B and C(hlgA, hlgB, 100 975 975 hglC) genes, complete cds 303 3 2367 3161gb|L01055| Staphylococcus aureus gamma-hemolysin components A, B and C(hlgA, hlgB, 99 793 795 hglC) genes, complete cds 305 1 1355 3dbj|D17366|STAA Staphylococcus aureus atl gene for autolysin, completecds and other ORFs 99 1343 1353 311 1 1315 2 gb|L42945| Staphylococcusaureus lytS and lytR genes, complete cds 98 1314 1314 312 6 7019 7870gb|L14017| Staphylococcus aureus methicillin-resistance protein (mecR)gene and 74 351 852 unknown ORF, complete cds 323 1 1003 8 gb|U31175|Staphylococcus aureus D-specific D-2-hydroxyacid dehydrogenase (ddh)gene, 98 996 996 complete cds 326 1 1 237 emb|Y00356|SASP Staphylococcusaureus V8 serine protease gene 100 108 237 338 1 388 89 emb|X64389|SALES. aureus leuF-P83 gene for F component of leucocidin R 98 259 300 338 21088 348 emb|X64389|SALE S. aureus leuF-P83 gene for F component ofleucocidin R 97 137 741 342 2 579 1754 gb|U06462| Staphylococcus aureusSA4 FtsZ (ftsZ) gene, complete cds 100 1176 1176 344 2 517 1248emb|V01281|SANU S. aureus mRNA for nuclease 98 732 732 349 1 230 3gb|M20393| S. aureus bacteriophage phi-11 attachment site (attB) 96 172228 353 1 516 16 gb|M83994| Staphylococcus aureus prolipoprotein signalpeptidase (lsp) gene, complete 100 187 501 cds 353 2 1046 510 gb|M83994|Staphylococcus aureus prolipoprotein signal peptidase (lsp) gene,complete 99 537 537 cds 356 1 3 674 gb|U20503| Staphylococcus aureus MHCclass II analog gene, complete cds 75 671 672 361 1 1 903 gb|L19298|Staphylococcus aureus phosphatidylinositol-specific phospholipase C(plc) 98 747 903 gene, complete cds 361 2 1103 1507 gb|L19298|Staphylococcus aureus phosphatidylinositol-specific phospholipase C(plc) 97 68 405 gene, complete cds 373 1 3 1148 emb|X62288|SAPE S.aureus DNA for penicillin-binding protein 2 99 1146 1146 389 3 1248 592emb|X62282|SATS S. aureus target site DNA for IS431 insertion 97 349 657400 1 1 540 emb|X61716|SAHL S. aureus hlb gene encoding sphingomyelinase99 389 540 400 2 1187 681 emb|X13404|SAHL Staphylococcus aureus hlb genefor beta-hemolysin 99 178 507 408 1 1049 288 gb|S76213| asp23 = alkalineshock protein 23 (methicillin resistant) [Staphylococcus 99 163 762aureus, 912, Genomic, 1360 nt] 418 1 2 217 gb|L41499| Staphylococcusaureus ORF1, partial cds, ORF2, ORF3, autolysin (at1) genes, 100 216 216complete cds 418 2 639 424 dbj|D17366|STAA Staphylococcus aureus at1gene for autolysin, complete cds and other ORFs 100 188 216 421 2 12622509 gb|L43098| Transposon Tn5404 and insertion sequences IS1181 andIS1182 (from 99 1248 1248 Staphylococcus aureus) DNA 422 1 2 325gb|K02985| S. aureus (strain RN450) transposon Tn554 insertion site 96200 324 427 1 434 3 dbj|D28879|STAP Staphylococcus aureus gene forpenicillin-binding protein 1, complete cds 100 432 432 427 2 1122 415dbj|D28879|STAP Staphylococcus aureus gene for penicillin-bindingprotein 1, complete cds 100 151 708 435 1 2 808 dbj|D86240|D862Staphylococcus aureus gene for unkown function and dlt operon dltA,dltB, 100 556 807 dltC and dltD genes,complete cds 435 2 832 999dbj|D86240|D862 Staphylococcus aureus gene for unkown function and dltoperon dltA, dltB, 100 134 168 dltC and dltD genes, complete cds 436 1685 29 emb|X17688|SAFE S. aureus factor essential for expression ofmethicillin resistance (femA) 97 657 657 gene, complete cds, and trpAgene, 3′ end 436 2 1657 911 emb|X17688|SAFE S. aureus factor essentialfor expression of methicillin resistance (femA) 100 294 747 gene,complete cds, and trpA gene, 3′ end 442 1 347 1300 emb|X72700|SAPV S.aureus genes for S and F components of Panton-Valentine leucocidins 84204 954 445 2 1906 2178 gb|L01055| Staphylococcus aureus gamma-hemolysincomponents A, B and C (hlgA, hlgB, 98 187 273 hglC) genes, complete cds447 1 167 1078 gb|U19770| Staphylococcus aureus pyrrolidone carboxylpeptidase (pcp) gene, complete 100 51 912 cds 447 2 1176 1784 gb|U19770|Staphylococcus aureus pyrrolidone carboxyl peptidase (pcp) gene,complete 96 597 609 cds 454 3 4319 1329 emb|Z18852|SACF S. aureus genefor clumping factor 75 653 2991 472 4 5479 3062 gb|L25288|Staphylococcus aureus gyrase-like protein alpha and beta subunit (grlAand 99 2418 2418 grlB) genes, complete cds 472 5 6792 5464 gb|L25288|Staphylococcus aureus gyrase-like protein alpha and beta subunit (grlAand 99 1328 1329 grlB) genes, complete cds 475 2 566 889 emb|X52543|SAAGS. aureus agrA, agrB and hld genes 100 76 324 481 4 1560 1198emb|X64172|SARP S. aureus rplL, orf202, rpoB(rif) and rpoC genes forribosomal protein 100 250 363 L7/L12, hypothetical protein ORF202,DNA-directed RNA polymerase beta & beta′ chains 481 5 1244 1534emb|X64172|SARP S. aureus rplL, orf202, rpoB(rif) and rpoC genes forribosomal protein 100 224 291 L7/L12, hypothetical protein ORF202,DNA-directed RNA polymerase beta & beta′ chains 487 2 1188 988gb|M83994| Staphylococcus aureus prolipoprotein signal peptidase (lsp)gene, complete 98 72 201 cds 489 1 1370 3 gb|U21221| Staphylococcusaureus hyaluronate lyase (hysA) gene, complete cds 99 1368 1368 503 2653 171 gb|M83994| Staphylococcus aureus prolipoprotein signal peptidase(lsp) gene, complete 100 108 483 cds 511 3 1613 2242 gb|L14017|Staphylococcus aureus methicillin-resistance protein (mecR) gene and 84323 630 unknown ORF, complete cds 511 4 2700 2278 gb|S76213| asp23 =alkaline shock protein 23 (methicillin resistant) [Staphylococcus 96 423423 aureus, 912, Genomic, 1360 nt] 520 2 758 1297 emb|X72014|SAFI S.aureus fib gene for fibrinogen-binding protein 99 540 540 520 3 14361801 emb|X72013|SAFI S. aureus fib gene for fibrinogen-binding protein99 221 366 526 1 1092 34 dbj|D17366|STAA Staphylococcus aureus atl genefor autolysin, complete cds and other ORFs 99 641 1059 528 2 58 963gb|L19300| Staphylococcus aureus DNA sequence encoding three ORFs,complete cds; 99 260 906 prophage phi-11 sequence homology, 5′ flank 5283 1098 2870 gb|L19300| Staphylococcus aureus DNA sequence encoding threeORFs, complete cds; 99 866 1773 prophage phi-11 sequence homology, 5′flank 530 1 3 434 gb|U31979| Staphylococcus aureus chorismate synthase(aroC) and nucleoside diphosphate 99 432 432 kinase (ndk) genes,complete cds, dehydroauinate synthase (aroB) and geranylgeranylpyrophosphate synthetase homolog (gerCC) genes, partial cds 530 2 12112395 gb|U31979| Staphylococcus aureus chorismate synthase (aroC) andnucleoside diphosphate 91 1185 1185 kinase (ndk) genes; complete cds,dehydroauinate synthase (aroB) and geranylgeranyl pyrophosphatesynthetase homolog (gerCC) genes, partial cds 530 3 2409 2801 gb|U31979|Staphylococcus aureus chorismate synthase (aroC) and nucleosidediphosphate 88 181 393 kinase (ndk) genes, complete cds, dehydroauinatesynthase (aroB) and geranylgeranyl pyrophosphate synthetase homolog(gerCC) genes, partial cds 530 4 2690 3484 gb|L05004| Staphylococcusaureus dehydroquinate synthase (aroB) gene, 3′ end cds; 3- 100 75 795phosphoshikimate-1-carboxyvinyltransferase (aroA) gene, complete cds;ORF3, complete cds 530 5 3482 4792 gb|L05004| Staphylococcus aureusdehydroquinate synthase (aroB) gene, 3′ end cds; 3- 99 905 1311phosphoshikimate-1-carboxyvinyltransferase (aroA) gene, complete cds;ORF3, complete cds 530 6 4790 5380 gb|L05004| Staphylococcus aureusdehydroquinate synthase (aroB) gene, 3′ end cds; 3- 100 196 591phosphoshikimate-1-carboxyvinyltransferase (aroA) gene, complete cds;ORF3, complete cds 539 1 3 338 emb|X76490|SAGL S. aureus (bb270) glnAand glnR genes 99 336 336 539 2 336 527 emb|X76490|SAGL S. aureus(bb270) glnA and glnR genes 100 189 192 554 1 365 3 gb|U73374|Staphylococcus aureus type 8 capsule genes, cap8A, cap8B, cap8C, cap8D,100 54 363 cap8E, cap8F, cap8G, cap8H, cap8I, cap8J, cap8K, cap8L,cap8M, cap8N, cap8O, cap8P, complete cds 554 2 1252 329 gb|U73374|Staphylococcus aureus type 8 capsule genes, cap8A, cap8B, cap8C, cap8D,99 918 924 cap8E, cap8F, cap8G, cap8H, cap8I, cap8J, cap8K, cap8L,cap8M, cap8N, cap8O, cap8P, complete cds 554 3 1374 1174 gb|U73374|Staphylococcus aureus type 8 capsule genes, cap8A, cap8B, cap8C, cap8D,96 122 201 cap8E, cap8F, cap8G, cap8H, cap8I, cap8J, cap8K, cap8L,cap8M, cap8N, cap8O, cap8P, complete cds 584 2 705 391 gb|U21221|Staphylococcus aureus hyaluronate lyase (hysA) gene, complete cds 99 306315 587 3 1475 4288 emb|Z18852|SACF S. aureus gene for clumping factor98 2588 2814 598 1 1953 25 dbj|D28879|STAP Staphylococcus aureus genefor penicillin-binding protein 1, complete cds 99 1873 1929 605 1 2 745dbj|D86240|D862 Staphylococcus aureus gene for unkown function and dltoperon dltA, dltB, 98 338 744 dltC and dltD genes, complete cds 609 1816 4 emb|X76490|SAGL S. aureus (bb270) glnA and glnR genes 100 495 813614 1 642 4 gb|M32103| Staphylococcus aureus lac repressor (lacR) gene,complete cds and lacA 99 639 639 repressor (lacA), partial cds 626 11255 2 gb|M63176| Staphylococcus aureus helicase required for T181replication (pcrA) gene, 100 225 1254 complete cds 626 2 2284 1253gb|M63176| Staphylococcus aureus helicase required for T181 replication(pcrA) gene, 99 838 1032 complete cds 629 1 1001 3 emb|X17688|SAFE S.aureus factor essential for expression of methicillin resistance (femA)99 990 999 gene, complete cds, and trpA gene, 3′ end 629 2 1195 983emb|X17688|SAFE S. aureus factor essential for expression of methicillinresistance (femA) 98 194 213 gene, complete cds, and trpA gene, 3′ end631 2 3228 1330 emb|Z18852|SACF S. aureus gene for clumping factor 82489 1899 632 1 3 551 emb|Z30588|SAST S. aureus (RN4220) genes forpotential ABC transporter and potential 99 549 549 membrane spanningprotein 632 2 529 1323 emb|Z30588|SAST S. aureus (RN4220) genes forpotential ABC transporter and potential 99 795 795 membrane spanningprotein 651 1 1070 231 gb|L19300| Staphylococcus aureus DNA sequenceencoding three ORFs, complete cds; 99 478 840 prophage phi-11 sequencehomology, 5′ flank 657 2 1105 410 gb|L14017| Staphylococcus aureusmethicillin-resistance protein (mecR) gene and 84 456 696 unknown ORF,complete cds 662 1 456 4 emb|X13404|SAHL Staphylococcus aureus hlb genefor beta-hemolysin 100 369 453 662 2 230 475 emb|X13404|SAHLStaphylococcus aureus hlb gene for beta-hemolysin 100 246 246 662 3 7461399 emb|X13404|SAHL Staphylococcus aureus hlb gene for beta-hemolysin99 653 654 682 1 480 4 gb|M63177| S. aureus sigma factor (plaC) gene,complete cds 100 136 477 685 1 592 2 gb|U65000| Staphylococcus aureustype-I signal peptidase SpsA (spsA) gene, and type-I 98 534 591 signalpeptidase SpsB (spaB) gene, complete cds 685 2 1153 590 gb|U65000|Staphylococcus aureus type-I signal peptidase SpsA (spsA) gene, andtype-I 96 564 564 signal peptidase SpsB (spsB) gene, complete cds 697 13 527 gb|M63177| S. aureus sigma factor (plaC) gene, complete cds 100195 525 697 2 485 784 gb|M63177| S. aureus sigma factor (plaC) gene,complete cds 97 280 300 710 1 15 503 dbj|D86240|D862 Staphylococcusaureus gene for unkown function and dlt operon dltA, dltB, 99 217 489dltC and dltD genes, complete cds 733 1 26 205 gb|M80252| Staphylococcusaureus norA1199 gene (which mediates active efflux of 97 140 180fluoroguinolones), complete cds 741 1 1197 658 dbj|D83951|STALStaphylococcus aureus DNA for LukM component, LukF-PV like component, 81522 540 complete cds 752 1 1 636 emb|Y00356|SASP Staphylococcus aureusV8 serine protease gene 99 618 636 752 2 588 956 emb|Y00356|SASPStaphylococcus aureus V8 serine protease gene 99 340 369 756 1 709 110emb|X01645|SATO Staphylococcus aureus (Wood 46) gene for alpha-toxin 98567 600 777 1 950 318 emb|Z49245|SA42 S. aureus partial sod gene forsuperoxide dismutase 99 429 633 780 1 557 3 gb|U20503| Staphylococcusaureus MHC class II analog gene, complete cds 86 550 555 784 1 73 687gb|U63529| Staphylococcus aureus novel antigen gene, complete cds 99 568615 797 1 182 544 dbj|D14711|STAH Staphylococcus aureus HSP10 and HSP60genes 98 363 363 798 1 302 72 emb|X58434|SAPD S. aureus pdhB, pdhC andpdhD genes for pyruvate decarboxylase, 95 196 231 dihydrolipoamideacetyltransferase and dihydrolipoamide dehydrogenase 823 1 3 467gb|S77055| recF cluster: dnaA = replisome assembly protein...gyrB = DNAgyrase beta 99 156 465 subunit [Staphylococcus aureus, YB886, Genomic, 5genes, 3573 nt] 848 1 175 2 gb|L25288| Staphylococcus aureus gyrase-likeprotein alpha and beta subunit (grlA and 99 174 174 grlB) genes,complete cds 848 2 318 160 gb|L25288| Staphylococcus aureus gyrase-likeprotein alpha and beta subunit (grlA and 100 131 159 grlB) genes,complete cds 866 1 397 2 emb|X64172|SARP S. aureus rplL, orf202,rpoB(rif) and rpoC genes for ribosomal protein 99 395 396 L7/L12,hypothetical protein ORF202, DNA-directed RNA polymerase beta & beta′chains 883 1 1 285 dbj|D90119|STAN S. aureus norA gene 99 131 285 884 1334 62 emb|X52543|SAAG S. aureus agrA, agrB and hld genes 98 265 273 8842 522 328 emb|X52543|SAAG S. aureus agrA, agrB and hld genes 100 195 195912 2 517 681 emb|Z30588|SAST S. aureus (RN4220) genes for potential ABCtransporter and potential 99 163 165 membrane spanning protein 917 1 2265 gb|M64724| S. aureus tagatose 6-phosphate isomerase gene, completecds 99 247 264 917 2 238 396 gb|M64724| S. aureus tagatose 6-phosphateisomerase gene, complete cds 95 147 159 918 1 1215 4 emb|X93205|SAPT S.aureus ptsH and ptsI genes 99 1212 1212 967 1 1 411 dbj|D90119|STAN S.aureus norA gene 97 395 411 991 1 337 2 emb|X52543|SAAG S. aureus agrA,agrB and hld genes 99 336 336 1000 1 845 573 gb|L14017| Staphylococcusaureus methicillin-resistance protein (mecR) gene and 78 190 273 unknownORF, complete cds 1001 1 265 32 dbj|D86240|D862 Staphylococcus aureusgene for unkown function and dlt operon dltA, dltB, 99 234 234 dltC anddltD genes, complete cds 1010 1 1 285 gb|U21221| Staphylococcus aureushyaluronate lyase (hysA) gene, complete cds 99 224 285 1046 1 330 4emb|X72700|SAPV S. aureus genes for S and F components ofPanton-Valentine leucocidins 85 205 327 1060 1 286 92 emb|X58434|SAPD S.aureus pdhB, pdhC and pdhD genes for pyruvate decarboxylase, 99 180 195dihydrolipoamide acetyltransferase and dihydrolipoamide dehydrogenase1073 1 589 2 gb|K02985| S. aureus (strain RN450) transposon Tn554insertion site 100 131 588 1079 1 3 230 dbj|D86240|D862 Staphylococcusaureus gene for unkown function and dlt operon dltA, dltB, 99 228 228dltC and dltD genes, complete cds 1079 2 218 484 dbj|D86240|D862Staphylococcus aureus gene for unkown function and dlt operon dltA,dltB, 100 267 267 dltC and dltD genes, complete cds 1079 3 460 645dbj|D86240|D862 Staphylococcus aureus gene for unkown function and dltoperon dltA, dltB, 100 186 186 dltC and dltD genes, complete cds 1092 1146 3 emb|X58434|SAPD S. aureus pdhB, pdhC and pdhD genes for pyruvatedecarboxylase, 98 124 144 dihydrolipoamide acetyltransferase anddihydrolipoamide dehydrogenase 1143 1 1 243 gb|M63177| S. aureus sigmafactor (plaC) gene, complete cds 99 243 243 1157 1 2 136 emb|Z48003|SADNS. aureus gene for DNA polymerase III 97 127 135 1189 1 361 2 gb|S74031|norA = NorA (ISP794) [Staphylococcus aureus, NCTC 8325, Insertion, 1820nt] 99 360 360 1190 1 2 283 gb|M21854| S. aureus agr gene encoding anaccessory gene regulator protein, complete 100 282 282 cds 1190 2 888649 emb|X52543|SAAG S. aureus agrA, agrB and hld genes 100 240 240 12251 2 163 emb|X17679|SACO Staphylococcus aureus coa gene for coagulase 97124 162 1243 1 2 529 dbj|D86240|D862 Staphylococcus aureus gene forunkown function and dlt operon dltA, dltB, 99 495 528 dltC and dltDgenes, complete cds 1244 1 1 210 gb|S74031| norA = NorA (ISP794)[Staphylococcus aureus, NCTC 8325, Insertion, 1820 nt] 100 210 210 13011 41 472 emb|X76490|SAGL S. aureus (bb270) glnA and glnR genes 99 299432 1315 1 18 326 emb|X64172|SARP S. aureus rplL, orf202, rpoB(rif) andrpoC genes for ribosomal protein 98 277 309 L7/L12, hypothetical proteinORF202, DNA-directed RNA polymerase beta & beta′ chains 1519 1 2 175dbj|D28879|STAP Staphylococcus aureus gene for penicillin-bindingprotein 1, complete cds 98 139 174 1663 1 675 4 dbj|D86240|D862Staphylococcus aureus gene for unkown function and dlt operon dltA,dltB, 98 672 672 dltC and dltD genes, complete cds 1797 1 324 4gb|U73374| Staphylococcus aureus type 8 capsule genes, cap8A, cap8B,cap8C, csp8D, 99 321 321 cap8E, cap8F, cap8G, cap8H, cap8I, cap8J,cap8K, cap8L, cap8M, cap8N, cap8O, cap8P, complete cds 1857 1 1 192gb|M90536| Staphylococcus aureus alpha-hemolysin gene, 3′ end 98 192 1921923 1 2 181 emb|X17688|SAFE S. aureus factor essential for expressionof methicillin resistance (femA) 100 180 180 gene, complete cds, andtrpA gene, 3′ end 1957 1 2 346 gb|U60589| Staphylococcus aureus novelantigen gene, complete cds 99 345 345 1988 1 1 402 dbj|D86240|D862Staphylococcus aureus gene for unkown function and dlt operon dltA,dltB, 100 402 402 dltC and dltD genes, complete cds 2100 1 208 2gb|M63177| S. aureus sigma factor (plaC) gene, complete cds 99 207 2072199 1 1 402 gb|U66664| Staphylococcus aureus DNA fragment with class IIpromoter activity 99 131 402 2537 1 156 4 emb|X17688|SAFE S. aureusfactor essential for expression of methicillin resistance (femA) 99 153153 gene, complete cds, and trpA gene, 3′ end 2891 1 2 400 gb|L25426|Staphylococcus aureus penicillin-binding protein 2 (pbp2) gene, complete99 399 399 cds 2950 1 398 18 dbj|D30690|STAN Staphylococcus aureus genesfor ORF37; HSP20; HSP70; HSP40; ORF35, complete 100 358 381 cds 2971 1 3398 gb|U51132| Staphylococcus aureus o-succinylbenzoic acid CoA ligase(mene), and o- 97 272 396 succinylbenzoic acid synthetase (menc) genes,complete cds 2978 1 328 38 gb|U31979| Staphylococcus aureus chorismatesynthase (aroC) and nucleoside diphosphate 98 250 291 kinase (ndk)genes, complete cds, dehydroauinate synthase (aroB) and geranylgeranylpyrophosphate synthetase homolog (gerCC) genes, partial cds 2985 1 46496 emb|X17679|SACO Staphylococcus aureus coa gene for coagulase 98 347369 3006 1 1784 1398 gb|U11779| Staphylococcus aureusmethicillin-resistant ATCC 33952 clone RRNV30 16S-23S 87 82 387 rRNAspacer region 3008 1 238 2 dbj|D30690|STAN Staphylococcus aureus genesfor ORF37; HSP20; HSP70; HSP40; ORF35, complete 88 178 237 cds 3008 2281 111 dbj|D30690|STAN Staphylococcus aureus genes for ORF37; HSP20;HSP70; HSP40; ORF35, complete 97 120 171 cds 3011 1 398 3emb|X62992|SAFN S. aureus fnbB gene for fibronectin binding protein B 9372 396 3019 1 2 235 gb|J03479| S. aureus enzyme III-lac (lacF), enzymeII-lac (lacE), and phospho-beta- 97 234 234 galactosidase (lacG) genes,complete cds 3023 1 81 233 gb|U06451| Staphylococcus aureus prolinepermease homolog (putP) gene, complete cds 87 100 153 3029 1 90 287gb|U51133| Staphylococcus aureus phosphoenolpyruvate carboxykinase(pcka) gene, 100 135 198 complete cds 3039 1 18 164 gb|U51133|Staphylococcus aureus phosphoenolpyruvate carboxykinase (pcka) gene, 97135 147 complete cds 3039 2 70 327 gb|U51133| Staphylococcus aureusphosphoenolpyruvate carboxykinase (pcka) gene, 77 183 258 complete cds3056 1 3 215 emb|X64172|SARP S. aureus rplL, orf202, rpoB(rif) and rpoCgenes for ribosomal protein 99 213 213 L7/L12, hypothetical proteinORF202, DNA-directed RNA polymerase beta & beta’ chains 3059 1 1 261dbj|D30690|STAN Staphylococcus aureus genes for ORF37; HSP20; HSP70;HSP40; ORF35, complete 98 234 261 cds 3073 1 27 284 gb|U06451|Staphylococcus aureus proline permease homolog (putP) gene, complete cds99 229 258 3074 1 2 397 emb|X64172|SARP S. aureus rplL, orf202,rpoB(rif) and rpoC genes for ribosomal protein 96 250 396 L7/L12,hypothetical protein ORF202, DNA-directed RNA polymerase beta & beta’chains 3088 1 3 239 dbj|D86727|D867 Staphylococcus aureus DNA for DNApolymerase III, complete cds 95 215 237 3097 1 244 44 emb|Z48003|SADN S.aureus gene for DNA polymerase III 97 160 201 3102 1 155 3 gb|J03479| S.aureus enzyme III-lac (lacF), enzyme II-lac (lacE), and phospho-beta- 97142 153 galactosidase (lacG) genes, complete cds 3121 1 398 228emb|X58434|SAPD S. aureus pdhB, pdhC and pdhD genes for pyruvatedecarboxylase, 100 88 171 dihydrolipoamide acetyltransferase anddihydrolipoamide dehydrogenase 3125 1 233 3 emb|X89233|SARP S. aureusDNA for rpoC gene 98 192 231 3133 1 2 175 emb|Z18852|SACF S. aureus genefor clumping factor 96 154 174 3160 1 211 2 dbj|D10489|STAGStaphylococcus aureus genes for DNA gyrase A and B, complete cds 89 197210 3176 1 1 378 emb|X58434|SAPD S. aureus pdhB, pdhC and pdhD genes forpyruvate decarboxylase, 96 91 378 dihydrolipoamide acetyltransferase anddihydrolipoamide dehydrogenase 3192 1 211 2 gb|J03479| S. aureus enzymeIII-lac (lacF), enzyme II-lac (lacE), and phospho-beta- 98 72 210galactosidase (lacG) genes, complete cds 3210 1 3 143 gb|M76714|Staphylococcus aureus peptidoglycan hydrolase gene, complete cds 96 141141 3232 3 1282 458 gb|L14017| Staphylococcus aureusmethicillin-resistance protein (mecR) gene and 71 257 825 unknown ORF,complete cds 3538 1 2 394 emb|X89233|SARP S. aureus DNA for rpoC gene 99350 393 3543 1 392 634 gb|L11530| Staphylococcus aureus transfer RNAsequence with two rRNAs 99 102 243 3555 1 320 3 emb|Z18852|SACF S.aureus gene for clumping factor 99 307 318 3559 1 3 182 emb|X17679|SACOStaphylococcus aureus coa gene for coagulase 100 141 180 3559 2 95 313emb|X17679|SACO Staphylococcus aureus coa gene for coagulase 98 174 2193563 1 141 4 gb|U35773| Staphylococcus aureus prolipoproteindiacylglyceryl transferase (lgt) gene, 100 79 138 complete cds 3563 2363 199 gb|U35773| Staphylococcus aureus prolipoprotein diacylglyceryltransferase (lgt) gene, 98 162 165 complete cds 3566 1 3 422emb|X16457|SAST Staphylococcus aureus gene for staphylocoagulase 98 175420 3588 1 2 262 gb|L43098| Transposon Tn5404 and insertion sequencesIS1181 and IS1182 (from 99 253 261 Staphylococcus aureus) DNA 3593 1 3350 gb|J03479| S. aureus enzyme III-lac (lacF), enzyme II-lac (lacE),and phospho-beta- 99 345 348 galactosidase (lacG) genes, complete cds3600 1 381 4 emb|Z18852|SACF S. aureus gene for clumping factor 72 346378 3602 1 396 4 emb|Z18852|SACF S. aureus gene for clumping factor 98319 393 3656 1 528 43 emb|Z18852|SACF S. aureus gene for clumping factor84 403 486 3682 1 3 236 emb|X64172|SARP S. aureus rplL, orf202,rpoB(rif) and rpoC genes for ribosomal protein 100 231 234 L7/L12,hypothetical protein ORF202, DNA-directed RNA polymerase beta & beta’chains 3682 2 224 415 emb|X64172|SARP S. aureus rplL, orf202, rpoB(rif)and rpoC genes for ribosomal protein 100 112 192 L7/L12, hypotheticalprotein ORF202, DNA-directed RNA polymerase beta & beta’ chains 3693 1423 88 emb|X62992|SAFN S. aureus fnbB gene for fibronectin bindingprotein B 100 229 336 3702 1 354 115 gb|L11530| Staphylococcus aureustransfer RNA sequence with two rRNAs 96 81 240 3725 1 463 2emb|Z18852|SACF S. aureus gene for clumping factor 71 367 462 3761 1 45091 gb|L14017| Staphylococcus aureus methicillin-resistance protein(mecR) gene and 85 333 360 unknown ORF, complete cds 3767 1 1 402emb|X64172|SARP S. aureus rplL, orf202, rpoB(rif) and rpoC genes forribosomal protein 98 387 402 L7/L12, hypothetical protein ORF202,DNA-directed RNA polymerase beta & beta’ chains 3775 1 2 286emb|X64172|SARP S. aureus rplL, orf202, rpoB(rif) and rpoC genes forribosomal protein 100 227 285 L7/L12, hypothetical protein ORF202,DNA-directed RNA polymerase beta & beta′ chains 3786 1 229 2dbj|D10489|STAG Staphylococcus aureus genes for DNA gyrase A and B,complete cds 100 204 228 3786 2 366 190 dbj|D10489|STAG Staphylococcusaureus genes for DNA gyrase A and B, complete cds 95 123 177 3798 1 3251 emb|X17679|SACO Staphylococcus aureus coa gene for coagulase 99 249249 3813 1 398 3 gb|J04151| S. aureus fibronectin-binding protein (fnbA)mRNA, complete cds 98 396 396 3819 1 184 402 emb|X68425|SA23 S. aureusgene for 23S rRNA 99 161 219 3844 1 468 4 gb|U48826| Staphylococcusaureus elastin binding protein (ebpS) gene, complete cds 87 204 465 38451 1 381 emb|X58434|SAPD S. aureus pdhB, pdhC and pdhD genes for pyruvatedecarboxylase, 94 356 381 dihydrolipoamide acetyltransferase anddihydrolipoamide dehydrogenase 3856 1 400 2 gb|L14017| Staphylococcusaureus methicillin-resistance protein (mecR) gene and 76 192 399 unknownORF, complete cds 3859 1 573 97 emb|Z18852|SACF S. aureus gene forclumping factor 85 347 477 3871 1 327 4 gb|M76714| Staphylococcus aureuspeptidoglycan hydrolase gene, complete cds 100 299 324 3876 1 2 253dbj|D10489|STAG Staphylococcus aureus genes for DNA gyrase A and B,complete cds 100 217 252 3877 1 288 4 gb|J03479| S. aureus enzymeIII-lac (lacF), enzyme II-lac (lacE), and phospho-beta- 97 209 285galactosidase (lacG) genes, complete cds 3878 1 1 237 emb|X58434|SAPD S.aureus pdhB, pdhC and pdhD genes for pyruvate decarboxylase, 96 155 237dihydrolipoamide acetyltransferase and dihydrolipoamide dehydrogenase3888 1 3 173 emb|X16457|SAST Staphylococcus aureus gene forstaphylocoagulase 98 171 171 3893 1 1 183 emb|X89233|SARP S. aureus DNAfor rpoC gene 100 170 183 3893 2 181 357 emb|X89233|SARP S. aureus DNAfor rpoC gene 98 79 177 3894 1 3 485 emb|X64172|SARP S. aureus rplL,orf202, rpoB(rif) and rpoC genes for ribosomal protein 99 450 483L7/L12, hypothetical protein ORF202, DNA-directed RNA polymerase beta &beta’ chains 3895 1 420 4 gb|J04151| S. aureus fibronectin-bindingprotein (fnbA) mRNA, complete cds 99 411 417 3905 1 48 239 gb|L05004|Staphylococcus aureus dehydroquinate synthase (aroB) gene, 3′ end cds;3- 100 159 192 phosphoshikimate-1-carboxyvinyltransferase (aroA) gene,complete cds; ORF3, complete cds 3905 2 188 400 gb|L05004|Staphylococcus aureus dehydroquinate synthase (aroB) gene, 3′ end cds;3- 97 88 213 phosphoshikimate-1-carboxyvinyltransferase (aroA) gene,complete cds; ORF3, complete cds 3910 1 3 359 emb|X58434|SAPD S. aureuspdhB, pdhC and pdhD genes for pyruvate decarboxylase, 99 278 357dihydrolipoamide acetyltransferase and dihydrolipoamide dehydrogenase3915 1 1 330 gb|L14017| Staphylococcus aureus methicillin-resistanceprotein (mecR) gene and 75 175 330 unknown ORF, complete cds 3964 1 3473 emb|Z48003|SADN S. aureus gene for DNA polymerase III 100 295 345 40071 199 390 emb|X16457|SAST Staphylococcus aureus gene forstaphylocoagulase 98 163 192 4036 1 3 371 dbj|D10489|STAG Staphylococcusaureus genes for DNA gyrase A and B, complete cds 99 339 369 4046 1 3484 emb|Z18852|SACF S. aureus gene for clumping factor 87 221 345 4060 1 1375 emb|Z18852|SACF S. aureus gene for clumping factor 96 271 375 4061 1432 4 emb|Z48003|SADN S. aureus gene for DNA polymerase III 99 429 4294062 1 304 2 gb|L14017| Staphylococcus aureus methicillin-resistanceprotein (mecR) gene and 75 198 303 unknown ORF, complete cds 4085 1 58402 gb|U11786| Staphylococcus aureus methicillin-resistant ATCC 33952clone RRNV42 16S-23S 98 127 345 rRNA spacer region 4088 1 2 301gb|L43098| Transposon Tn5404 and insertion sequences IS1181 and IS1182(from 99 227 300 Staphylococcus aureus) DNA 4093 1 2 277 emb|X58434|SAPDS. aureus pdhB, pdhC and pdhD genes for pyruvate decarboxylase, 99 276276 dihydrolipoamide acetyltransferase and dihydrolipoamidedehydrogenase 4097 1 1 402 emb|Z18852|SACF S. aureus gene for clumpingfactor 74 307 402 4116 1 22 402 gb|L05004| Staphylococcus aureusdehydroquinate synthase (aroB) gene, 3′ end cds; 3- 98 157 381phosphoshikimate-1-carboxyvinyltransferase (aroA) gene, complete cds;ORF3, complete cds 4125 1 240 401 gb|U73374| Staphylococcus aureus type8 capsule genes, cap8A, cap8B, cap8C, cap8D, 100 86 162 cap8E, cap8F,cap8G, cap8H, cap8I, cap8J, cap8K, cap8L, cap8M, cap8N, cap8O, cap8P,complete cds 4149 1 35 247 gb|J04151| S. aureus fibronectin-bindingprotein (fnbA) mRNA, complete cds 99 200 213 4151 1 366 103 gb|L14017|Staphylococcus aureus methicillin-resistance protein (mecR) gene and 87150 264 unknown ORF, complete cds 4154 1 398 42 emb|X64172|SARP S.aureus rplL, orf202, rpoB(rif) and rpoC genes for ribosomal protein 99297 357 L7/L12, hypothetical protein ORF202, DNA-directed RNA polymerasebeta & beta’ chains 4179 1 1 294 emb|X64172|SARP S. aureus rplL, orf202,rpoB(rif) and rpoC genes for ribosomal protein 98 240 294 L7/L12,hypothetical protein ORF202, DNA-directed RNA polymerase beta & beta’chains 4203 1 1 255 emb|X89233|SARP S. aureus DNA for rpoC gene 99 239255 4206 1 1 303 emb|Z18852|SACF S. aureus gene for clumping factor 100236 303 4206 2 195 344 emb|Z18852|SACF S. aureus gene for clumpingfactor 95 65 150 4208 1 108 314 emb|X58434|SAPD S. aureus pdhB, pdhC andpdhD genes for pyruvate decarboxylase, 89 76 207 dihydrolipoamideacetyltransferase and dihydrolipoamide dehydrogenase 4216 1 330 4emb|X58434|SAPD S. aureus pdhB, pdhC and pdhD genes for pyruvatedecarboxylase, 98 326 327 dihydrolipoamide acetyltransferase anddihydrolipoamide dehydrogenase 4226 1 298 2 gb|L11530| Staphylococcusaureus transfer RNA sequence with two rRNAs 97 132 297 4260 1 216 383gb|U11784| Staphylococcus aureus methicillin-resistant ATCC 33952 cloneRRNV40 16S-23S 83 141 168 rRNA spacer region 4272 1 179 3emb|Z48003|SADN S. aureus gene for DNA polymerase III 100 164 177 4276 14 177 emb|X16457|SAST Staphylococcus aureus gene for staphylocoagulase99 150 174 4277 1 1 270 emb|X64172|SARP S. aureus rplL, orf202,rpoB(rif) and rpoC genes for ribosomal protein 99 265 270 L7/L12,hypothetical protein ORF202, DNA-directed RNA polymerase beta & beta’chains 4282 1 377 63 emb|X64172|SARP S. aureus rplL, orf202, rpoB(rif)and rpoC genes for ribosomal protein 98 282 315 L7/L12, hypotheticalprotein ORF202, DNA-directed RNA polymerase beta & beta’ chains 4291 1191 3 emb|X64172|SARP S. aureus rplL, orf202, rpoB(rif) and rpoC genesfor ribosomal protein 99 183 189 L7/L12, hypothetical protein ORF202,DNA-directed RNA polymerase beta & beta’ chains 4295 1 3 329emb|X16457|SAST Staphylococcus aureus gene for staphylocoagulase 94 144327 4313 1 280 125 gb|L11530| Staphylococcus aureus transfer RNAsequence with two rRNAs 100 94 156 4315 1 3 185 gb|J03479| S. aureusenzyme III-lac (lacF), enzyme II-lac (lacE), and phospho-beta- 100 158183 galactosidase (lacG) genes, complete cds 4315 2 101 310 gb|J03479|S. aureus enzyme III-lac (lacF), enzyme II-lac (lacE), and phospho-beta-98 75 210 galactosidase (lacG) genes, complete cds 4327 1 1 294gb|L43098| Transposon Tn5404 and insertion sequences IS1181 and IS1182(from 98 294 294 Staphylococcus aureus) DNA 4360 1 319 35 gb|U02910|Staphylococcus aureus ATCC 25923 16S rRNA gene, partial sequence 100 116285 4364 1 3 146 emb|X64172|SARP S. aureus rplL, orf202, rpoB(rif) andrpoC genes for ribosomal protein 95 140 144 L7/L12, hypothetical proteinORF202, DNA-directed RNA polymerase beta & beta’ chains 4388 1 167 310emb|X62992|SAFN S. aureus fnbB gene for fibronectin binding protein B 73119 144 4401 1 2 313 emb|X62992|SAFN S. aureus fnbB gene for fibronectinbinding protein B 97 243 312 4421 1 36 281 dbj|D12572|STA2Staphylococcus aureus rrnA gene for 23S ribosomal RNA 100 112 246 4426 13 293 emb|Z18852|SACF S. aureus gene for clumping factor 85 185 291 44281 248 3 emb|X64172|SARP S. aureus rplL, orf202, rpoB(rif) and rpoC genesfor ribosomal protein 100 139 246 L7/L12, hypothetical protein ORF202,DNA-directed RNA polymerase beta & beta′ chains 4462 1 2 271emb|X64172|SARP S. aureus rplL, orf202, rpoB(rif) and rpoC genes forribosomal protein 99 270 270 L7/L12, hypothetical protein ORF202,DNA-directed RNA polymerase beta & beta′ chains 4466 1 1 240emb|Z18852|SACF S. aureus gene for clumping factor 99 231 240 4469 1 1312 gb|J03479| S. aureus enzyme III-lac (lacF), enzyme II-lac (lacE),and phospho-beta- 99 265 312 galactosidase (lacG) genes, complete cds4485 1 3 263 gb|L43098| Transposon Tn5404 and insertion sequences IS1181and IS1182 (from 98 259 261 Staphylococcus aureus) DNA 4492 1 74 400gb|M86227| Staphylococcus aureus DNA gyrase B subunit (gyrB) RecFhomologue (recF) and 85 104 327 DNA gyrase A subunit (gyrA) gene,complete cds 4497 1 269 3 emb|Z18852|SACF S. aureus gene for clumpingfactor 99 213 267 4529 1 2 172 emb|X64172|SARP S. aureus rplL, orf202,rpoB(rif) and rpoC genes for ribosomal protein 100 151 171 L7/L12,hypothetical protein ORF202, DNA-directed RNA polymerase beta & beta′chains 4547 1 1 300 emb|X62992|SAFN S. aureus fnbB gene for fibronectinbinding protein B 100 157 300 4554 1 160 2 emb|Z18852|SACF S. aureusgene for clumping factor 84 126 159 4565 1 9 227 emb|Z18852|SACF S.aureus gene for clumping factor 84 213 219 4569 1 79 222 emb|Z18852|SACFS. aureus gene for clumping factor 98 127 144 4608 1 22 216emb|X58434|SAPD S. aureus pdhB, pdhC and pdhD genes for pyruvatedecarboxylase, 92 168 195 dihydrolipoamide acetyltransferase anddihydrolipoamide dehydrogenase 4614 1 234 4 emb|Z18852|SACF S. aureusgene for clumping factor 86 169 231 4623 1 105 302 gb|J04151| S. aureusfibronectin-binding protein (fnbA) mRNA, complete cds 99 152 198 4632 118 206 gb|J03479| S. aureus enzyme III-lac (lacF), enzyme II-lac (lacE),and phospho-beta- 98 183 189 galactosidase (lacG) genes, complete cds4646 1 1 222 emb|Z18852|SACF S. aureus gene for clumping factor 84 100222 4687 1 2 166 gb|J04151| S. aureus fibronectin-binding protein (fnbA)mRNA, complete cds 98 156 165 4695 1 158 3 gb|L14017| Staphylococcusaureus methicillin-resistance protein (mecR) gene and 75 155 156 unknownORF, complete cds 4703 1 1 153 emb|X58434|SAPD S. aureus pdhB, pdhC andpdhD genes for pyruvate decarboxylase, 98 103 153 dihydrolipoamideacetyltransferase and dihydrolipoamide dehydrogenase

[0289] TABLE 2 S. aureus - Putative coding regions of novel proteinssimilar to known proteins Start Stop match Contig ID ORF ID (nt) (nt)acession match gene name % sim % ident length (nt) 20 6 4679 4269gi|511839 ORF1 [Staphylococcus bacteriophage phi 11] 100 100 411 149 31577 1122 pir|B49703|B497 int gene activator RinA - bacteriophage phi 11100 100 456 149 5 1912 1715 gi|166161 Bacteriophage phi-11 int geneactivator [Staphylococcus acteriophage phi 100 100 198 11] 349 2 409 260gi|166159 integrase (int) [Staphylococcus bacteriophage phi 11] 100 100150 398 1 707 42 gi|166159 integrase (int) [Staphylococcus bacteriophagephi 11] 100 99 666 398 2 783 1001 gi|455128 excisionase (xis)[Staphylococcus bacteriophage phi 11] 100 100 219 502 4 1744 1574gi|1204912 H. influenzae predicted coding region HI0660 [Haemophilusinfluenzae] 100 71 171 849 1 2 262 gi|1373002 polyprotein [Bean commonmosaic virus] 100 46 261 1349 1 140 3 gi|143359 protein synthesisinitiation factor 2 (infB) [Bacillus subtilis] gi|49319 100 82 138 IF2gene product [Bacillus subtilis] 2880 1 21 308 gi|862933 protein kinaseC inhibitor-I [Homo sapiens] 100 98 288 3085 1 216 4 gi|1354211PET112-like protein [Bacillus subtilis] 100 100 213 4168 2 398 225gi|1354211 PET112-like protein [Bacillus subtilis] 100 100 174 331 1 2247 gi|426473 nusG gene product [Staphylococcus carnosus] 98 95 246 2072 1272 1463 gi|460259 enolase [Bacillus subtilis] 97 90 192 331 2 395850 gi|581638 L11 protein [Staphylococcus carnosus] 97 93 456 366 1 39215 gi|166161 Bacteriophage phi-11 int gene activator [Staphylococcusacteriophage phi 97 95 177 11] 680 3 718 936 gi|426473 nusG gene product[Staphylococcus carnosus] 97 97 219 3578 1 144 4 gi|1339950 largesubunit of NADH-dependent glutamate synthase [Plectonema boryanum] 97 79141 157 1 321 518 gi|1022726 unknown [Staphylococcus haemolyticus] 96 88198 205 33 16147 15824 gi|1165302 S10 [Bacillus subtilis] 96 91 324 39191 48 401 gi|871784 Clp-like ATP-dependent protease binding subunit [Bostaurus] 96 81 354 4133 1 417 4 gi|1022726 unknown [Staphylococcushaemolyticus] 96 84 414 4168 1 355 2 gi|1354211 PET112-like protein[Bacillus subtilis] 96 95 354 4207 1 157 2 gi|602031 similar totrimethylamine DH [Mycoplasma capricolum]pir|S49950|S49950 96 86 156probable trimethylamine dehydrogenase (EC .5.99.7) - Mycoplasmacapricolum (SGC3) (fragment) 4227 2 152 331 gi|871784 Clp-likeATP-dependent protease binding subunit [Bos taurus] 96 81 180 4416 1 2862 gi|1022726 unknown [Staphylococcus haemolyticus] 96 84 285 22 1 430 2gi|511070 UreG [Staphylococcus xylosus] 95 88 429 22 7 4036 3710gi|581787 urease gamma subunit [Staphylococcus xylosus] 95 79 327 82 68794 9114 pir|JG0008|JG00 ribosomal protein S7 - Bacillusstearothermophilus 95 83 321 154 9 7838 6396 gi|1354211 PET112-likeprotein [Bacillus subtilis] 95 92 1443 186 3 2055 1312 gi|1514656 serine0-acetyltransferase [Staphylococcus xylosus] 95 87 744 205 5 4014 3622gi|142462 ribosomal protein S11 [Bacillus subtilis] 95 85 393 205 7 47934569 gi|142459 initiation factor 1 [Bacillus subtilis] 95 84 225 205 2110991 10617 gi|1044974 ribosomal protein L14 [Bacillus subtilis] 95 93375 259 5 6644 6000 sp|P47995|YSEA_(—) HYPOTHETICAL PROTEIN IN SECA5′REGION (ORF1) (FRAGMENT). 95 85 645 302 3 795 1097 gi|40186 homologousto E. coli ribosomal protein L27 [Bacillus subtilis] i|143592 L27 95 89303 ribosomal protein [Bacillus subtilis] ir|C21895|C21895 ribosomalprotein L27 - Bacillus subtilis p|P05657|RL27_BACSU 50S RIBOSOMALPROTEIN L27 (BL30) (BL24). i|40175 L24 gene prod 310 1 579 1523gi|1177684 chorismate mutase [Staphylococcus xylosus] 95 92 945 414 1 2163 pir|C48396|C483 ribosomal protein L34 - Bacillus stearothermophilus95 90 162 4185 2 125 277 gi|1276841 glutamate synthase (GOGAT) [Porphyrapurpurea] 95 86 153 22 2 723 418 gi|511069 UreF [Staphylococcus xylosus]94 91 306 22 5 3310 1574 gi|410516 urease alpha subunit [Staphylococcusxylosus] 94 85 1737 60 4 815 1372 gi|666116 glucose kinase[Staphylococcus xylosus] 94 87 558 205 18 9536 9060 gi|1044978 ribosomalprotein S8 [Bacillus subtilis] 94 78 477 326 4 2542 1706 gi|557492dihydroxynapthoic acid (DHNA) synthetase [Bacillus subtilis] gi|14318694 85 837 dihydroxynapthoic acid (DHNA) synthetase [Bacillus subtilis]414 3 737 955 gi|467386 thiophen and furan oxidation [Bacillus subtilis]94 77 219 426 3 1823 1386 gi|1263908 putative [Staphylococcusepidermidis] 94 87 438 534 1 2 355 gi|633650 enzyme II(mannitol)[Staphylococcus carnosus] 94 84 354 1017 1 2 229 gi|149435 putative[Lactococcus lactis] 94 73 228 3098 1 184 38 gi|413952 ipa-28d geneproduct [Bacillus subtilis] 94 50 147 3232 1 316 2 gi|1022725 unknown[Staphylococcus haemolyticus] 94 84 315 42 5 2089 2259 pir|B48396|B483ribosomal protein L33 - Bacillus stearothermophilus 93 81 171 101 2 13831021 gi|155345 arsenic efflux pump protein [Plasmid pSX267] 93 82 363205 24 11865 11503 sp|P14577|RL16_(—) 50S RIBOSOMAL PROTEIN L16. 93 83363 259 4 5673 3055 gi|499335 secA protein [Staphylococcus carnosus] 9385 2619 275 1 1114 2 gi|633650 enzyme II(mannitol) [Staphylococcuscarnosus] 93 86 1113 444 6 5773 5339 gi|1022726 unknown [Staphylococcushaemolyticus] 93 81 435 491 1 152 622 gi|46912 ribosomal protein L13[Staphylococcus carnosus] 93 88 471 607 6 1674 2033 gi|1022726 unknown[Staphylococcus haemolyticus] 93 83 360 653 1 488 3 gi|580890translation initiation factor IF3 (AA 1-172) [Bacillustearothermophilus] 93 77 486 1864 1 3 194 gi|306553 ribosmal proteinsmall subunit [Homo sapiens] 93 93 192 2997 1 28 300 gi|143390 carbamylphosphate synthetase [Bacillus subtilis] 93 82 273 3232 2 596 285gi|1022725 unknown [Staphylococcus haemolyticus] 93 84 312 3761 2 621448 gi|1022725 unknown [Staphylococcus haemolyticus] 93 88 174 16 1 3374 gi|142781 putative cytoplasmic protein; putative [Bacillus subtilis]92 83 372 sp|P37954|UVRB_BACSU EXCINUCLEASE ABC SUBUNIT B (DINA PROTEIN)FRAGMENT). 31 7 5915 6124 gi|1136430 KIAA0185 protein [Homo sapiens] 9246 210 56 19 26483 27391 gi|467401 unknown [Bacillus subtilis] 92 80 90969 6 5882 6130 gi|530200 trophoblastin [Ovis aries] 92 53 249 145 3 20381508 gi|1022725 unknown [Staphylococcus haemolyticus] 92 80 531 171 32362 1964 gi|517475 D-amino acid transaminase [Staphylococcushaemolyticus] 92 86 399 205 12 6962 6429 gi|49189 secY gene product[Staphylococcus carnosus] 92 85 534 205 19 10255 9698 gi|1044976ribosomal protein L5 [Bacillus subtilis] 92 82 558 219 1 357 4gi|1303812 YqeV [Bacillus subtilis] 92 88 354 344 3 1575 1805 gi|1405474CspC protein [Bacillus cereus] 92 85 231 699 1 20 361 gi|413999 ipa-75dgene product [Bacillus subtilis] 92 81 342 1343 1 2 160 pir|A45434|A454ribosomal protein L19 - Bacillus stearothermophilus 92 84 159 1958 1 2644 gi|407908 EIIscr [Staphylococcus xylosus] 92 80 261 3578 2 386 54gi|1339950 large subunit of NADH-dependent glutamate synthase[Plectonema boryanum] 92 78 333 3585 1 324 4 gi|1339950 large subunit ofNADH-dependent glutamate synthase [Plectonema boryanum] 92 81 321 3640 14 402 gi|1022726 unknown [Staphylococcus haemolyticus] 92 81 399 4362 114 178 gi|450688 hsdM gene of EcoprrI gene product [Escherichia coli]pir|S38437|S38437 hsdM 92 78 165 protein - Escherichia colipir|S09629|S09629 hypothetical protein A - Escherichia coli (SUB 40-520)4446 1 182 6 gi|1022725 unknown [Staphylococcus haemolyticus] 92 82 1774549 1 232 2 gi|1022726 unknown [Staphylococcus haemolyticus] 92 80 2314626 1 3 224 gi|1022725 unknown [Staphylococcus haemolyticus] 92 84 2222 4 3980 4531 gi|535349 Codw [Bacillus subtilis] 91 74 552 28 1 2 1126gi|1001376 hypothetical protein [Synechocystis sp.] 91 78 1125 60 5 13541701 gi|1226043 orf2 downstream of glucose kinase [Staphylococcusxylosus] 91 80 348 101 1 1036 83 gi|150728 arsenic efflux pump protein[Plasmid pI258] 91 80 954 187 2 412 1194 gi|142559 ATP synthase alphasubunit [Bacillus megaterium] 91 79 783 205 22 11298 11017 gi|40149 S17protein (AA 1-87) [Bacillus subtilis] 91 83 282 206 7 8184 10262gi|1072418 glcA gene product [Staphylococcus carnosus] 91 83 2079 306 22326 767 gi|143012 GMP synthetase [Bacillus subtilis] 91 78 1560 306 33826 2333 gi|467399 IMP dehydrogenase [Bacillus subtilis] 91 79 1494 3103 2194 3207 gi|1177685 ccpA gene product [Staphylococcus xylosus] 91 811014 343 4 2974 3150 gi|949974 sucrose repressor [Staphylococcusxylosus] 91 82 177 480 3 1606 3042 gi|433991 ATP synthase subunit beta[Bacillus subtilis] 91 85 1437 536 3 1280 534 gi|143366 adenylosuccinatelyase (PUR-B) [Bacillus subtilis] pir|C29326|WZBSDS 91 79 747adenylosuccinate lyase (EC 4.3.2.2) - Bacillus subtilis 552 1 615 166gi|297874 fructose-bisphosphate aldolase [Staphylococcus carnosus]pir|A49943|A49943 91 79 450 fructose-bisphosphate aldolase (EC4.1.2.13) - Staphylococcus carnosus (strain TM300) 637 1 1 1536gi|143597 CTP synthetase [Bacillus subtilis] 91 79 1536 859 1 21 359gi|385178 unknown [Bacillus subtilis] 91 66 339 1327 1 339 530 gi|496558orfX [Bacillus subtilis] 91 71 192 2515 1 275 84 gi|511070 UreG[Staphylococcus xylosus] 91 85 192 2594 1 2 202 gi|146824beta-cystathionase [Escherichia coli] 91 75 201 3764 1 425 3 gi|1022725unknown [Staphylococcus haemolyticus] 91 78 423 4011 1 127 495gi|1022726 unknown [Staphylococcus haemolyticus] 91 79 369 4227 1 1 177gi|296464 ATPase [Lactococcus lactis] 91 66 177 42 3 815 1033 gi|520401catalase [Haemophilus influenzae] 90 86 219 51 8 3717 4607 gi|580899OppF gene product [Bacillus subtilis] 90 74 891 129 3 4001 2685gi|1146206 glutamate dehydrogenase [Bacillus subtilis] 90 76 1317 164 1716628 16933 sp|P05766|RS15_(—) 30S RIBOSOMAL PROTEIN S15 (BS18) 90 74306 171 5 2819 2655 gi|517475 D-amino acid transaminase [Staphylococcushaemolyticus] 90 78 165 205 4 3550 2603 gi|142463 RNA polymerasealpha-core-subunit [Bacillus subtilis] 90 76 948 205 6 4410 4072gi|1044989 ribosomal protein S13 [Bacillus subtilis] 90 73 339 205 106404 5643 gi|49189 secY gene product [Staphylococcus carnosus] 90 81 762205 11 6472 6299 gi|49189 secY gene product [Staphylococcus carnosus] 9078 174 205 27 13345 12998 gi|786157 Ribosomal Protein S19 [Bacillussubtilis] 90 79 348 205 31 15496 15134 gi|1165303 L3 [Bacillus subtilis]90 79 363 260 5 5773 4523 gi|1161380 IcaA [Staphylococcus epidermidis]90 78 1251 299 6 3378 3947 gi|467440 ‘phosphoribosylpyrophosphatesynthetase [Bacillus subtilis] gi|40218 PRPP 90 78 570 synthetase (AA1-317) [Bacillus subtilis] 320 2 1025 1717 gi|312443 carbamoyl-phosphatesynthase (glutamine-hydrolysing) [Bacillus aldolyticus] 90 75 693 330 41581 1769 gi|986963 beta-tubulin [Sporidiobolus pararoseus] 90 80 189369 1 523 92 pir|S34762|S347 L-serine dehydratase beta chain -Clostridium sp. 90 77 432 557 1 3 188 gi|1511589 M. jannaschii predictedcoding region MJ1624 [Methanococcus jannaschii] 90 54 186 663 2 667 1200gi|143786 tryptophanyl-tRNA synthetase (EC 6.1.1.2) [Bacillus subtilis]90 73 534 pir|JT0481|YWBS tryptophan-tRNA ligase (EC 6.1.1.2) - Bacillussubtilis 717 1 1 261 gi|143065 hubst [Bacillus stearothermophilus] 90 79261 745 4 865 671 gi|1205433 H. influenzae predicted coding regionHI1190 [Haemophilus influenzae] 90 81 195 1007 1 386 565 gi|143366adenylosuccinate lyase (PUR-B) [Bacillus subtilis] pir|C29326|WZBSDS 9077 180 adenylosuccinate lyase EC 4.3.2.2) - Bacillus subtilis 1054 1 33183 gi|1033122 ORF_f729 [Escherichia coli] 90 50 249 1156 1 117 707gi|1477776 ClpP [Bacillus subtilis] 90 80 591 1180 1 205 2 gi|1377831unknown [Bacillus subtilis] 90 74 204 1253 1 1 462 gi|40046phosphoglucose isomerase A (AA 1-449) [Bacillus stearothermophilus] 9075 462 ir|S15936|NUBSSA glucose-6-phosphate isomerase (EC 5.3.1.9) A -Bacillus stearothermophilus 2951 1 3 269 gi|144816formyltetrahydrofolate synthetase (FTHFS) (ttg start codon) (EC .3.4.3)90 76 267 [Moorella thermoacetica] 3140 1 166 5 gi|1070014protein-dependent [Bacillus subtilis] 90 52 162 4594 1 3 233 gi|871784Clp-like ATP-dependent protease binding subunit [Bos taurus] 90 76 23187 1 1028 1750 gi|467327 unknown [Bacillus subtilis] 89 75 723 112 1 2505 gi|153741 ATP-binding protein [Streptococcus mutans] 89 77 504 118 1120 398 gi|1303804 YqeQ [Bacillus subtilis] 89 75 279 128 4 3545 3757gi|460257 triose phosphate isomerase [Bacillus subtilis] 89 84 213 16412 11667 12755 gi|39954 IF2 (aa 1-741) [Bacillus stearothermophilus] 8980 1089 205 13 7405 6935 gi|216338 ORF for L15 ribosomal protein[Bacillus subtilis] 89 76 471 205 32 15823 15494 gi|1165303 L3 [Bacillussubtilis] 89 80 330 270 3 2207 2007 pir|C41902|C419 arsenate reductase(EC 1,—,—,—) - Staphylococcus xylosus plasmid pSX267 89 81 201 395 2 157672 gi|520574 glutamate racemase [Staphylococcus haemolyticus] 89 80 516494 1 3 839 gi|396259 protease [Staphylococcus epidermidis] 89 77 837510 1 1 444 gi|40046 phosphoglucose isomerase A (AA 1-449) [Bacillusstearothermophilus] 89 74 444 ir|S15936|NUBSSA glucose-6-phosphateisomerase (EC 5.3.1.9) A - Bacillus stearothermophilus 615 1 1210 296gi|1303812 YqeV [Bacillus subtilis] 89 74 915 841 1 18 341 gi|1165303 L3[Bacillus subtilis] 89 80 324 1111 1 352 813 gi|47146 thermonuclease[Staphylococcus intermedius] 89 70 462 1875 1 2 256 gi|1205108ATP-dependent protease binding subunit [Haemophilus influenzae] 89 82255 2963 1 11 367 gi|467458 cell division protein [Bacillus subtilis] 8983 357 3020 1 90 362 gi|1239988 hypothetical protein [Bacillus subtilis]89 66 273 3565 1 2 400 gi|1256635 dihydroxy-acid dehydratase [Bacillussubtilis] 89 75 399 3586 1 105 314 gi|580832 ATP synthase subunit gamma[Bacillus subtilis] 89 82 210 3629 1 399 4 gi|1009366 Respiratorynitrate reductase [Bacillus subtilis] 89 78 396 3688 1 2 400 gi|1146206glutamate dehydrogenase [Bacillus subtilis] 89 75 399 3699 1 399 4gi|1339950 large subunit of NADH-dependent glutamate synthase[Plectonema boryanum] 89 75 396 4016 1 216 4 gi|1009366 Respiratorynitrate reductase [Bacillus subtilis] 89 71 213 4177 1 301 131 gi|149426putative [Lactococcus lactis] 89 76 171 4436 1 302 3 gi|1022725 unknown[Staphylococcus haemolyticus] 89 80 300 4635 1 162 4 gi|1022725 unknown[Staphylococcus haemolyticus] 89 73 159 2 2 1330 2676 gi|520754 putative[Bacillus subtilis] 88 76 1347 42 2 468 848 sp|P42321|CATA_(—) CATALASE(EC 1.11.1.6). 88 76 381 53 5 4722 3055 gi|474177alpha-D-1,4-glucosidase [Staphylococcus xylosus] 88 80 1668 56 16 1801818617 gi|467411 recombination protein [Bacillus subtilis] 88 77 600 60 3376 843 gi|666116 glucose kinase [Staphylococcus xylosus] 88 77 468 70 21245 907 gi|44095 replication initiator protein [Listeria monocytogenes]88 74 339 82 8 11514 12719 pir|A60663|A606 translation elongation factorTu - Bacillus subtilis 88 79 1206 103 7 4179 4391 gi|167181serine/threonine kinase receptor [Brassica napus] 88 77 213 114 8 77328232 gi|1022726 unknown [Staphylococcus haemolyticus] 88 72 501 118 2308 2011 gi|1303804 YqeQ [Bacillus subtilis] 88 77 1704 141 3 657 1136gi|1405446 transketolase [Bacillus subtilis] 88 72 480 148 7 5871 6116gi|1118002 dihydropteroate synthase [Staphylococcus haemolyticus] 88 78246 165 3 1428 2231 gi|40053 phenylalanyl-tRNA synthetase alpha subunit[Bacillus subtilis] 88 80 804 ir|S11730|YFBSA phenylalanine-tRNA ligase(EC 6.1.1.20) alpha ain - Bacillus subtilis 205 28 14185 13343gi|1165306 L2 [Bacillus subtilis] 88 82 843 225 1 898 227 gi|1303840YqfS [Bacillus subtilis] 88 78 672 235 1 2 1975 gi|452309 valyl-tRNAsynthetase [Bacillus subtilis] 88 76 1974 339 3 1566 1072 gi|1118002dihydropteroate synthase [Staphylococcus haemolyticus] 88 73 495 443 42928 1531 gi|558559 pyrimidine nucleoside phosphorylase [Bacillussubtilis] 88 73 1398 532 1 3 419 gi|143797 valyl-tRNA synthetase[Bacillus stearothermophilus]sp|P11931|SYV_BACST 88 78 417 VALYL-TRNASYNTHETASE (EC 6.1.1.9) VALINE-TRNA LIGASE) (VALRS). 534 3 2504 2968gi|153049 mannitol-specific enzyme-III [Staphylococcuscarnosus]pir|JQ0088|JQ0088 88 82 465 phosphotransferase system enzyme II(EC .7.1.69), mannitol-specific, factor III - Staphylococcus carnosussp|P17876|PTMA_STACA PTS SYSTEM, MANNITOL-SPECIFIC IIA COMPONENTEIIA-MTL) ( 705 2 399 214 gi|710018 nitrite reductase (nirB) [Bacillussubtilis] 88 70 186 1000 2 1309 794 gi|1022726 unknown [Staphylococcushaemolyticus] 88 78 516 1299 1 324 61 gi|401786 phosphomannomutase[Mycoplasma pirum] 88 55 264 1341 2 170 400 gi|39963 ribosomal proteinL20 (AA 1-119) [Bacillus stearothermophilus] 88 82 231 ir|S05348|R5BS20ribosomal protein L20 - Bacillus stearothermophilus 1386 1 41 214pir|B47154|B471 signal recognition particle 54 K chain homolog Ffh -Bacillus subtilis 88 71 174 1386 2 183 533 pir|B47154|B471 signalrecognition particle 54 K chain homolog Ffh - Bacillus subtilis 88 73351 2949 1 399 94 gi|535350 CodX [Bacillus subtilis] 88 73 306 2984 1 5169 gi|218277 O-acetylserine(thiol) lyase [Spinacia oleracea] 88 70 1653035 1 1 138 gi|493083 dihydroxyacetone kinase [Citrobacter freundii] 8867 138 3089 1 3 152 gi|606055 ORF_f746 [Escherichia coli] 88 88 150 39171 410 3 gi|143378 pyruvate decarboxylase (E-1) beta subunit [Bacillussubtilis]gi|1377836 88 77 408 pyruvate decarboxylase E-1 beta subunit[Bacillus subtilis] 4199 1 342 4 gi|1405454 aconitase [Bacillussubtilis] 88 82 339 4201 1 369 4 gi|515938 glutamate synthase(ferredoxin) [Synechocystis sp.]pir|S46957|S46957 88 84 366 glutamatesynthase (ferredoxin) (EC 1.4.7.1) - ynechocystis sp. 4274 1 1 336gi|515938 glutamate synthase (ferredoxin) [Synechocystissp.]pir|S46957|S46957 88 84 336 glutamate synthase (ferredoxin) (EC1.4.7.1) - ynechocystis sp. 4308 1 399 4 gi|1146206 glutamatedehydrogenase [Bacillus subtilis] 88 71 396 2 5 4570 6000 gi|535350 CodX[Bacillus subtilis] 87 70 1431 52 8 6482 6183 gi|1064791 functionumknown [Bacillus subtilis] 87 66 300 73 3 1584 2480 gi|142992 glycerolkinase (glpK) (EC 2.7.1.30) [Bacillus subtilis] pir|B45868|B45868 87 72897 glycerol kinase (EC 2.7.1.30) - Bacillus subtilissp|P18157|GLPK_BACSU GLYCEROL KINASE (EC 2.7.1.30) (ATP:GLYCEROL-PHOSPHOTRANSFERASE) (GLYCEROKINASE) (GK). 98 12 8813 9100gi|467433 unknown [Bacillus subtilis] 87 62 288 124 4 2988 1711gi|556886 serine hydroxymethyltransferase [Bacillus subtilis]pir|S49363|S49363 87 77 1278 serine hydroxymethyltransferase - Bacillussubtilis 124 6 4032 3607 gi|556883 Unknown [Bacillus subtilis] 87 66 426148 5 3741 4559 gi|467460 unknown [Bacillus subtilis] 87 70 819 164 1312710 13810 gi|39954 IF2 (aa 1-741) [Bacillus stearothermophilus] 87 721101 177 2 1104 2126 gi|467385 unknown [Bacillus subtilis] 87 78 1023199 1 1158 334 gi|143527 iron-sulfur protein [Bacillus subtilis] 87 77825 199 2 2933 1149 pir|A27763|A277 succinate dehydrogenase (EC1.3.99.1) flavoprotein - Bacillus subtilis 87 80 1785 205 23 11543 11304gi|1044972 ribosomal protein L29 [Bacillus subtilis] 87 78 240 205 2512607 11939 gi|1165309 S3 [Bacillus subtilis] 87 75 669 222 1 1107 181gi|1177249 rec233 gene product [Bacillus subtilis] 87 70 927 236 3 13331031 gi|1146198 ferredoxin [Bacillus subtilis] 87 80 303 246 5 2292 1999gi|467373 ribosomal protein S18 [Bacillus subtilis] 87 77 294 260 2 34222655 gi|1161382 IcaC [Staphylococcus epidermidis] 87 72 768 320 3 16962391 gi|312443 carbamoyl-phosphate synthase (glutamine-hydrolysing)[Bacillus aldolyticus] 87 80 696 380 4 1165 1383 gi|142570 ATP synthasec subunit [Bacillus firmus] 87 80 219 414 4 900 1073 gi|467386 thiophenand furan oxidation [Bacillus subtilis] 87 77 174 425 2 794 585gi|1046166 pilin repressor [Mycoplasma genitalium] 87 69 210 448 1 722189 gi|405134 acetate kinase [Bacillus subtilis] 87 75 534 480 1 1 711gi|142559 ATP synthase alpha subunit [Bacillus megaterium] 87 79 711 4811 2 352 sp|Q06797|RL1_B 50S RIBOSOMAL PROTEIN L1 (BL1). 87 72 351 677 2359 955 gi|460911 fructose-bisphosphate aldolase [Bacillus subtilis] 8778 597 677 3 934 1284 gi|460911 fructose-bisphosphate aldolase [Bacillussubtilis] 87 78 351 876 1 3 452 gi|1146247 asparaginyl-tRNA synthetase[Bacillus subtilis] 87 79 450 1376 1 214 2 gi|1065555 F46H6.4 geneproduct [Caenorhabditis elegans] 87 75 213 2206 1 3 374 gi|215098excisionase [Bacteriophage 154a] 87 72 372 2938 1 3 290 gi|508979GTP-binding protein [Bacillus subtilis] 87 69 288 3081 2 126 308gi|467399 IMP dehydrogenase [Bacillus subtilis] 87 72 183 3535 1 3 401gi|1405454 aconitase [Bacillus subtilis] 87 80 399 4238 1 275 3gi|603769 HutU protein, urocanase [Bacillus subtilis] 87 73 273 4 8 87367045 gi|603769 HutU protein, urocanase [Bacillus subtilis] 86 72 1692 226 3738 3286 gi|410515 urease beta subunit [Staphylococcus xylosus] 86 73453 54 2 1572 664 gi|289287 UDP-glucose pyrophosphorylase [Bacillussubtilis] 86 70 909 124 3 1713 1090 gi|556887 uracilphosphoribosyltransferase [Bacillus subtilis] pir|S49364|S49364 86 74624 uracil phosphoribosyltransferase - Bacillus subtilis 148 3 1349 3448gi|467458 cell division protein [Bacillus subtilis] 86 75 2100 148 43638 3859 gi|467460 unknown [Bacillus subtilis] 86 73 222 152 3 13402086 gi|1377835 pyruvate decarboxylase E-1 alpha subunit [Bacillussubtilis] 86 75 747 164 18 17347 19467 gi|1184680 polynucleotidephosphorylase [Bacillus subtilis] 86 72 2121 180 2 554 1159 gi|143467ribosomal protein S4 [Bacillus subtilis] 86 80 606 205 3 2592 2218gi|142464 ribosomal protein L17 [Bacillus subtilis] 86 77 375 205 2612990 12616 gi|40107 ribosomal protein L22 [Bacillus stearothermophilus]ir|S10612|S10612 86 75 375 ribosomal protein L22 - Bacillusstearothermophilus 246 7 3140 2817 gi|467375 ribosomal protein S6[Bacillus subtilis] 86 70 324 299 3 1196 1540 gi|39656 spoVG geneproduct [Bacillus megaterium] 86 70 345 299 7 3884 4345 gi|467440‘phosphoribosylpyrophosphate synthetase [Bacillus subtilis] gi|40218PRPP 86 78 462 synthetase (AA 1-317) [Bacillus subtilis] 304 5 2170 2523gi|666983 putative ATP binding subunit [Bacillus subtilis] 86 65 354 3102 1487 1678 gi|1177684 chorismate mutase [Staphylococcus xylosus] 86 71192 337 5 2086 3405 gi|487434 isocitrate dehydrogenase [Bacillussubtilis] 86 78 1320 339 2 1109 729 gi|1118003 dihydroneopterin aldolase[Staphylococcus haemolyticus] 86 77 381 358 2 2124 3440 gi|1146219 28.2%of identity to the Escherichia coli GTP-binding protein Era; putative 8673 1317 [Bacillus subtilis] 404 2 1015 2058 gi|1303817 YqfA [Bacillussubtilis] 86 78 1044 581 2 452 243 gi|40056 phoP gene product [Bacillussubtilis] 86 71 210 642 2 338 1075 gi|1176399 EpiF [Staphylococcusepidermidis] 86 72 738 770 1 347 72 gi|143328 phoP protein (put.);putative [Bacillus subtilis] 86 69 276 865 1 890 3 gi|1146247asparaginyl-tRNA synthetase [Bacillus subtilis] 86 74 888 868 2 963 1133gi|1002911 transmembrane protein [Saccharomyces cerevisiae] 86 69 171904 1 1 162 gi|1303912 YqhW [Bacillus subtilis] 86 72 162 989 1 35 433gi|1303993 YqkL [Bacillus subtilis] 86 76 399 1212 1 150 4 gi|414014ipa-90d gene product [Bacillus subtilis] 86 70 147 1323 1 2 148 gi|40041pyruvate dehydrogenase (lipoamide) [Bacillus stearothermophilus] 86 75147 ir|S10798|DEBSPF pyruvate dehydrogenase (lipoamide) (EC 1.2.4.1) phachain - Bacillus stearothermophilus 3085 2 310 80 gi|1354211 PET112-likeprotein [Bacillus subtilis] 86 86 231 3847 1 1 228 gi|296464 ATPase[Lactococcus lactis] 86 63 228 4487 1 240 4 gi|1022726 unknown[Staphylococcus haemolyticus] 86 73 237 4583 1 187 2 gi|1022725 unknown[Staphylococcus haemolyticus] 86 79 186 25 5 4287 5039 gi|15024213-ketoacyl-acyl carrier protein reductase [Bacillus subtilis] 85 64 75356 21 29395 28163 gi|1408507 pyrimidine nucleoside transport protein[Bacillus subtilis] 85 69 1233 68 2 332 1192 gi|467376 unknown [Bacillussubtilis] 85 74 861 73 2 880 1707 gi|142992 glycerol kinase (glpK) (EC2.7.1.30) [Bacillus subtilis] pir|B45868|B45868 85 72 828 glycerolkinase (EC 2.7.1.30) - Bacillus subtilis sp|P18157|GLPK_BACSU GLYCEROLKINASE (EC 2.7.1.30) (ATP: GLYCEROL-PHOSPHOTRANSFERASE) (GLYCEROKINASE)(GK). 106 4 1505 3490 gi|143766 (thrSv) (EC 6.1.1.3) [Bacillus subtilis]85 74 1986 128 2 1153 2202 gi|311924 glycerladehyde-3-phosphatedehydrogenase [Clostridium pasteurianum] 85 75 1050 pir|S34254|S34254glyceraldehyde-3-phosphate dehydrogenase (EC .2.1.12) - Clostridiumpasteurianum 129 4 5252 4038 gi|1064807 ORTHININE AMINOTRANSFERASE[Bacillus subtilis] 85 73 1215 138 6 3475 5673 gi|1072419 glcB geneproduct [Staphylococcus carnosus] 85 74 2199 189 1 2 169 gi|467385unknown [Bacillus subtilis] 85 65 168 205 15 8106 7588 gi|1044981ribosomal protein S5 [Bacillus subtilis] 85 75 519 205 20 10596 10264pir|A02819|R5BS ribosomal protein L24 - Bacillus stearothermophilus 8572 333 220 6 6101 5712 gi|48980 secA gene product [Bacillus subtilis] 8566 390 231 4 3159 1441 gi|1002520 MutS [Bacillus subtilis] 85 70 1719243 9 8013 8783 gi|414011 ipa-87r gene product [Bacillus subtilis] 85 72771 249 2 3186 478 gi|1405454 aconitase [Bacillus subtilis] 85 73 2709302 1 140 475 gi|40173 homolog of E. coli ribosomal protein L21[Bacillus subtilis] 85 72 336 ir|S18439|S18439 Ribosomal protein L21 -Bacillus subtilis p|P26908|RL21_BACSU 50S RIBOSOMAL PROTEIN L21 [BL20].333 1 2968 491 gi|442360 ClpC adenosine triphosphatase [Bacillussubtilis] 85 69 2478 364 6 6082 8196 gi|871784 Clp-like ATP-dependentprotease binding subunit [Bos taurus] 85 68 2115 448 2 1339 686gi|405134 acetate kinase [Bacillus subtilis] 85 68 654 747 1 853 455gi|1373157 orf-X; hypothetical protein; Method: conceptual translationsupplied by 85 73 399 author [Bacillus subtilis] 886 2 159 467 gi|541768hemin permease [Yersinia enterocolitica] 85 55 309 1089 1 606 4pir|B47154|B471 signal recognition particle 54K chain homolog Ffh -Bacillus subtilis 85 71 603 1163 1 409 2 gi|304155 diaminopimelatedecarboxylase [Bacillus methanolicus] sp|P41023|DCDA_BACMT 85 62 408DIAMINOPIMELATE DECARBOXYLASE (EC 4.1.1.20) DAP DECARBOXYLASE]. 1924 1251 15 gi|215098 excisionase [Bacteriophage 154a] 85 73 237 2932 1 390 4gi|1041099 Pyruvate Kinase [Bacillus licheniformis] 85 71 387 3030 1 3275 gi|42370 pyruvate formate-lyase [AA 1-760] [Escherichia coli]ir|S01788|S01788 85 74 273 formate C-acetyltransferase (EC 2.3.1.54) -Escherichia coli 3111 1 299 3 gi|63568 limb deformity protein [Gallusgallus] 85 85 297 3778 1 316 2 gi|391840 beta-subunit of HDT[Pseudomonas fragi] 85 67 315 3835 1 1 387 gi|1204472 type I restrictionenzyme ECOR124/3 I M protein [Haemophilus influenzae] 85 56 387 4042 1 3386 gi|18178 formare acetyltransferase [Chlamydomonas reinhardtii]ir|S24997|S24997 85 70 384 formate C-acetyltransferase (EC 2.3.1.54) -Chlamydomonas reinhardtii 4053 1 35 340 gi|1204472 type I restrictionenzyme ECOR124/3 I M protein [Haemophilus influenzae] 85 56 306 4108 1 2181 gi|1072418 glcA gene product [Staphylococcus carnosus] 85 61 1804300 1 330 85 gi|151932 fructose enzyme II [Rhodobacter capsulatus] 8559 246 4392 1 355 83 gi|1022725 unknown [Staphylococcus haemolyticus] 8574 273 4408 1 2 235 gi|871784 Clp-like ATP-dependent protease bindingsubunit [Bos taurus] 85 62 234 4430 1 291 4 gi|1009366 Respiratorynitrate reductase [Bacillus subtilis] 85 68 288 4555 1 2 253 gi|450688hsdM gene of EcoprrI gene product [Escherichia coli] pir|S38437|S38437hsdM 85 52 252 protein - Escherichia coli pir|S09629|S09629 hypotheticalprotein A - Escherichia coli (SUB 40-520) 4611 1 242 3 gi|1256635dihydroxy-acid dehydratase [Bacillus subtilis] 85 65 240 4 10 1006110591 gi|46982 fosB gene product [Staphylococcus epidermidis] 84 68 53113 2 1172 996 gi|142450 ahrC protein [Bacillus subtilis] 84 56 177 16 41803 4652 gi|1277198 DNA repair protein [Deinococcus radiodurans] 84 672850 22 3 1128 721 gi|511069 UreF [Staphylococcus xylosus] 84 73 408 237 5055 5306 gi|603320 Yer082p [Saccharomyces cerevisiae] 84 61 252 53 1111145 10693 gi|1303948 YqiW [Bacillus subtilis] 84 68 453 53 12 1277011481 gi|142613 branched chain alpha-keto acid dehydrogenase E2[Bacillus subtilis] 84 71 1290 gi|1303944 BfmBB [Bacillus subtilis] 70 1982 632 gi|46647 ORF (repE) [Staphylococcus aureus] 84 68 351 73 4 25124311 gi|142993 glycerol-3-phosphate dehydrogenase (glpD) (EC 1.1.99.5)[Bacillus subtilis] 84 74 1800 98 7 4324 6096 gi|467427 methionyl-tRNAsynthetase [Bacillus subtilis] 84 66 1773 100 9 8680 7859 gi|1340128ORF1 [Staphylococcus aureus] 84 78 822 117 3 1934 3208 gi|1237019 Srb[Bacillus subtilis] 84 68 1275 148 6 4720 5670 gi|467462 cysteinesynthetase A [Bacillus subtilis] 84 69 951 152 4 2064 2456 gi|143377pyruvate decarboxylase (E-1) alpha subunit [Bacillus subtilis] 84 70 393pir|B36718|DEBSPA pyruvate dehydrogenase (lipoamide) (EC 1.2.4.1) lphachain - Bacillus subtilis 169 7 3634 3861 gi|1001342 hypotheticalprotein [Synechocystis sp.] 84 66 228 171 4 2657 2322 gi|517475 D-aminoacid transaminase [Staphylococcus haemolyticus] 84 71 336 186 6 62165491 gi|467475 unknown [Bacillus subtilis] 84 70 726 205 9 5692 5123gi|216340 ORF for adenylate kinase [Bacillus subtilis] 84 71 570 224 2915 1391 gi|288269 beta-fructofuranosidase [Staphylococcus xylosus] 8470 477 251 1 92 388 gi|1303790 YqeI [Bacillus subtilis] 84 65 297 282 31526 2836 gi|143040 glutamate-1-semialdehyde 2,1-aminotransferase[Bacillus subtilis] 84 75 1311 pir|D42728|D42728glutamate-1-semialdehyde 2,1-aminomutase (EC.4.3.8) - Bacillus subtilis307 5 2959 2780 gi|1070014 protein-dependent [Bacillus subtilis] 84 62180 320 4 2343 4229 gi|143390 carbamyl phosphate synthetase [Bacillussubtilis] 84 70 1887 372 1 3 296 gi|1022725 unknown [Staphylococcushaemolyticus] 84 70 294 413 2 1341 481 gi|1256146 YbbQ [Bacillussubtilis] 84 65 861 439 1 3 392 gi|1046173 osmotically inducible protein[Mycoplasma genitalium] 84 53 390 461 3 1362 2270 gi|40211 threoninesynthase (thrC) (AA 1-352) [Bacillus subtilis] ir|A25364|A25364 84 69909 threonine synthase (EC 4.2.99.2) - Bacillus subtilis 487 1 3 299gi|1144531 integrin-like protein alpha Intlp [Candida albicans] 84 46297 491 2 624 905 pir|S08564|R3BS ribosomal protein S9 - Bacillusstearothermophilus 84 69 282 491 3 836 1033 pir|S08564|R3BS ribosomalprotein S9 - Bacillus stearothermophilus 84 77 198 548 1 3 341 gi|431231uracil permease [Bacillus caldolyticus] 84 74 339 728 2 1748 795gi|912445 DNA polymerase [Bacillus caldotenax] 84 68 954 769 1 3 257gi|1510953 cobalamin biosynthesis protein N [Methanococcus jannaschii]84 38 255 954 1 156 4 gi|1405454 aconitase [Bacillus subtilis] 84 57 153957 1 3 395 gi|143402 recombination protein (ttg start codon) [Bacillussubtilis] gi|1303923 RecN 84 68 393 [Bacillus subtilis] 975 1 3 452gi|885934 ClpB [Synechococcus sp.] 84 70 450 1585 1 3 257 gi|510140ligoendopeptidase F [Lactococcus lactis] 84 56 255 2954 1 3 323gi|603769 HutU protein, urocanase [Bacillus subtilis] 84 73 321 2996 1348 46 gi|18178 formate acetyltransferase [Chlamydomonas reinhardtii]ir|S24997|S24997 84 65 303 formate C-acetyltransferase (EC 2.3.1.54) -Chlamydomonas reinhardtii 3766 1 375 13 gi|517205 67 kDaMyosin-crossreactive streptococcal antigen [Streptococcus yogenes] 84 72363 4022 1 2 169 gi|1146206 glutamate dehydrogenase [Bacillus subtilis]84 54 168 4058 1 312 4 gi|151932 fructose enzyme II [Rhodobactercapsulatus] 84 71 309 4108 2 106 351 gi|1072418 glcA gene product[Staphylococcus carnosus] 84 77 246 4183 1 3 308 gi|603769 HutU protein,urocanase [Bacillus subtilis] 84 72 306 4726 1 55 234 gi|146208glutamate synthase large subunit (EC 2.6.1.53) [Escherichia coli] 84 73180 pir|A29617|A29617 glutamate synthase (NADPH) (EC 1.4.1.13) largehain - Escherichia coli 22 4 1576 1109 gi|393297 urease accessoryprotein [Bacillus sp.] 83 64 468 53 13 13745 12768 gi|142612 branchedchain alpha-keto acid dehydrogenase E1-beta [Bacillus subtilis] 83 68978 57 16 12872 12387 gi|143132 lactate dehydrogenase (AC 1.1.1.27)[Bacillus caldolyticus] 83 66 486 pir|B29704|B29704 L-lactatedehydrogenase (EC 1.1.1.27) - Bacillus aldolyticus 66 3 2274 1429gi|1303894 YqhM [Bacillus subtilis] 83 63 846 66 5 4643 3168 gi|1212730YqhK [Bacillus subtilis] 83 68 1476 70 3 1523 1182 gi|44095 replicationinitiator protein [Listeria monocytogenes] 83 73 342 90 1 377 1429gi|155571 alcohol dehydrogenase I (adhA) (EC 1.1.1.1) [Zymomonasmobilis] 83 70 1053 pir|A35260|A35260 alcohol dehydrogenase (EC 1.1.1.1)I - Zymomonas obilis 95 2 708 2162 gi|506381 phospho-beta-glucosidase[Bacillus subtilis] 83 70 1455 137 1 68 694 gi|467391 initiation proteinof replicaton [Bacillus subtilis] 83 77 627 140 4 2742 2275 gi|634107kdpB [Escherichia coli] 83 65 468 142 3 2989 2510 gi|1212776 lumazinesynthase (b-subunit) [Bacillus amyloliquefaciens] 83 69 480 161 12 57496696 gi|903307 ORF75 [Bacillus subtilis] 83 64 948 164 9 9880 11070gi|49316 ORF2 gene product [Bacillus subtilis] 83 66 1191 164 14 1414814546 gi|580902 ORF6 gene product [Bacillus subtilis] 83 60 399 170 22467 1790 gi|520844 orf4 [Bacillus subtilis] 83 64 678 186 2 1370 711gi|289284 cysteinyl-tRNA synthetase [Bacillus subtilis] 83 72 660 205 147607 7392 gi|216337 ORF for L30 ribosomal protein [Bacillus subtilis] 8374 216 237 6 3683 4540 gi|1510488 imidazoleglycerol-phosphate synthase(cyclase) [Methanococcus jannaschii] 83 60 858 301 1 638 291 gi|467419unknown [Bacillus subtilis] 83 65 348 302 4 1421 2743 gi|508979GTP-binding protein [Bacillus subtilis] 83 68 1323 321 4 3571 3209gi|39844 fumarase (citG) (aa 1-462) [Bacillus subtilis] 83 68 363 367 12 352 gi|1039479 ORFU [Lactococcus lactis] 83 54 351 387 1 3 662gi|806281 DNA polymerase I [Bacillus stearothermophilus] 83 70 660 527 2916 1566 gi|396259 protease [Staphylococcus epidermidis] 83 67 651 533 1179 3 gi|142455 alanine dehydrogenase (EC 1.4.1.1) [Bacillusstearothermophilus] 83 66 177 pir|B34261|B34261 alanine dehydrogenase(EC 1.4.1.1) - Bacillus stearothermophilus 536 4 1438 1259 gi|143366adenylosuccinate lyase (PUR-B) [Bacillus subtilis] pir|C29326|WZBSDS 8367 180 adenylosuccinate lyase (EC 4.3.2.2) - Bacillus subtilis 652 1 2859 gi|520753 DNA topoisomerase I [Bacillus subtilis] 83 72 858 774 2200 361 gi|1522665 M. jannaschii predicted coding region MJECL28[Methanococcus jannaschii] 83 58 162 897 1 120 296 gi|1064807 ORTHININEAMINOTRANSFERASE [Bacillus subtilis] 83 76 177 1213 1 3 491 gi|289288lexA [Bacillus subtilis] 83 67 489 2529 1 150 4 gi|143786tryptophanyl-tRNA synthetase (EC 6.1.1.2) [Bacillus subtilis] 83 69 147pir|JT0481|YWBS tryptophan - tRNA ligase (EC 6.1.1.2) - Bacillussubtilis 2973 1 326 3 gi|1109687 ProZ [Bacillus subtilis] 83 58 324 30091 366 4 gi|882532 ORF_o294 [Escherichia coli] 83 65 363 3035 2 45 305gi|950062 hypothetical yeast protein 1 [Mycoplasma capricolum]pir|S48578|S48578 83 59 261 hypothetical protein - Mycoplasma capricolumSGC3) (fragment) 3906 1 67 309 gi|1353197 thioredoxin reductase[Eubacterium acidaminophilum] 83 61 243 4458 1 271 2 gi|397526 clumpingfactor [Staphylococcus aureus] 83 78 270 4570 1 223 2 gi|1022726 unknown[Staphylococcus haemolyticus] 83 74 222 4654 1 97 261 gi|1072419 glcBgene product [Staphylococcus carnosus] 83 79 165 16 2 295 1191 gi|153854uvs402 protein [Streptococcus pneumoniae] 82 67 897 16 3 1193 1798gi|153854 uvs402 protein [Streptococcus pneumoniae] 82 70 606 38 12 87247804 gi|1204400 N-acetylneuraminate lyase [Haemophilus influenzae] 82 58921 42 4 988 2019 gi|841192 catalase [Bacteroides fragilis] 82 70 103251 6 2590 3489 gi|143607 sporulation protein [Bacillus subtilis] 82 69900 56 11 12270 13925 gi|39431 oligo-1,6-glucosidase [Bacillus cereus]82 60 1656 56 15 17673 18014 gi|467410 unknown [Bacillus subtilis] 82 66342 61 2 881 3313 gi|143148 transfer RNA-Leu synthetase [Bacillussubtilis] 82 70 2433 82 7 9162 11318 gi|48240 elongation factor G (AA1-691) [Thermus aquaticus thermophilus] 82 64 2157 ir|S15928|EFTWGtranslation elongation factor G - Thermus aquaticus p|P13551|EFG_THETHELONGATION FACTOR G (EF-G). 85 2 3260 1050 gi|143369phosphoribosylformyl glycinamidine synthetase II (PUR-Q) [Bacillussubtilis] 82 66 2211 102 6 3662 5380 gi|1256635 dihydroxy-aciddehydratase [Bacillus subtilis| 82 65 1719 117 4 3242 3493pir|A47154|A471 orf1 5′ of Ffh - Bacillus subtilis 82 53 252 128 6 43775933 gi|460258 phosphoglycerate mutase [Bacillus subtilis] 82 66 1557129 2 1229 2182 gi|403373 glycerophosphoryl diester phosphodiesterase[Bacillus subtilis] 82 62 954 pir|S37251|S37251 glycerophosphoryldiester phosphodiesterase -Bacillus subtilis 170 1 2 1441 gi|1377831unknown [Bacillus subtilis] 82 67 1440 177 1 3 1094 gi|467386 thiophenand furan oxidation [Bacillus subtilis] 82 65 1092 184 4 3572 4039gi|153566 ORF (19 K protein) [Enterococcus faecalis] 82 59 468 189 84225 3995 gi|1001878 CspL protein [Listeria monocytogenes] 82 73 231 20619 20707 20048 gi|473916 lipopeptide antibiotics iturin A [Bacillussubtilis]sp|P39144|LP14_BACSU 82 50 660 LIPOPEPTIDE ANTIBIOTICS ITURIN AAND SURFACTIN IOSYNTHESIS PROTEIN. 221 2 805 1722 gi|517205 67 kDaMyosin-crossreactive streptococcal antigen [Streptococcus yogenes] 82 63918 223 4 3651 3436 gi|439619 [Salmonella typhimurium IS200 insertionsequence from SARA17, artial.], 82 69 216 gene product [Salmonellatyphimurium] 260 3 4296 3385 gi|1161381 IcaB [Staphylococcusepidermidis] 82 61 912 315 3 2855 846 gi|143397 quinol oxidase [Bacillussubtilis] 82 67 2010 321 10 7945 7370 gi|142981 ORF5; This ORF includesa region (aa23-103) containing a potential ron- 82 62 576 sulphur centrehomologous to a region of Rhodospirillum rubrum nd Chromatium vinosum;putative [Bacillus stearothermophilus] pir|PQ0299|PQ0299 hypotheticalprotein 5 (gldA 3′ region) - 331 3 1055 1342 gi|436574 ribosomal proteinL1 [Bacillus subtilis] 82 71 288 370 2 262 618 gi|1303793 YqeL [Bacillussubtilis] 82 59 357 404 4 3053 4024 gi|1303821 YqfE [Bacillus subtilis]82 68 972 405 4 3073 1706 gi|1303913 YqhX [Bacillus subtilis] 82 67 1368436 3 2864 1632 gi|149521 tryptophan synthase beta subunit [Lactococcuslactis]pir|S35129|S35129 82 67 1233 tryptophan synthase (EC 4.2.1.20)beta chain - Lactococcus lactis subsp. lactis 441 4 2573 1752 gi|142952glyceraldehyde-3-phosphate dehydrogenase [Bacillus tearothermophilus] 8267 822 444 12 10415 11227 gi|1204354 spore germination and vegetativegrowth protein [Haemophilus influenzae] 82 67 813 446 1 3 191 gi|143387aspartate transcarbamylase [Bacillus subtilis] 82 66 189 462 3 1007 1210gi|142521 deoxyribodipyrimidine photolyase [Bacillus subtilis]pir|A37192|A37192 uvrB 82 64 204 protein - Bacillus subtilissp|P14951|UVRC_BACSU EXCINUCLEASE ABC SUBUNIT C. 537 1 784 8 gi|853767UDP-N-acetylglucosamine 1-carboxyvinyltransferase [Bacillus subtilis] 8261 777 680 2 407 700 gi|426472 secE gene product [Staphylococcuscarnosus] 82 69 294 724 2 386 207 gi|143373 phosphoribosylaminoimidazole carboxy formyl ormyltransferase/inosine 82 68 180monophosphate cyclohydrolase (PUR-H(J)) Bacillus subtilis) 763 1 213 4gi|467458 cell division protein [Bacillus subtilis] 82 35 210 818 1 2832 gi|1064787 function unknown [Bacillus subtilis] 82 69 282 858 1 1751176 gi|143043 uroporphyrinogen decarboxylase [Bacillus subtilis]pir|B47045|B47045 82 71 1002 uroporphyrinogen decarboxylase (EC4.1.1.37) - Bacillus subtilis 895 1 3 599 gi|1027507 ATP binding protein[Borrelia burgdorferi] 82 72 597 939 1 10 399 gi|143795 transfer RNA-Tyrsynthetase [Bacillus subtilis] 82 60 390 961 1 1 306 gi|577647gamma-hemolysin [Staphylococcus aureus] 82 69 306 1192 1 155 3 gi|146974NH3-dependent NAD synthetase [Escherichia coli] 82 71 153 1317 1 49 375gi|407908 EIIscr [Staphylococcus xylosus] 82 72 327 1341 1 1 150gi|39962 ribosomal protein L35 (AA 1-66) [Bacillus stearothermophilus]82 68 150 ir|S05347|R5BS35 ribosomal protein L35 - Bacillusearothermophilus 2990 2 349 131 gi|534855 ATPase subunit epsilon[Bacillus stearothermophilus]sp|P42009|ATPE_BACST 82 47 219 ATP SYNTHASEEPSILON CHAIN (EC 3.6.1.34). 3024 1 45 224 gi|467402 unknown [Bacillussubtilis] 82 64 180 3045 1 139 2 gi|467335 ribosomal protein L9[Bacillus subtilis] 82 60 138 3045 2 400 242 gi|467335 ribosomal proteinL9 [Bacillus subtilis] 82 82 159 3091 1 238 2 gi|499335 secA protein[Staphylococcus carnosus] 82 78 237 3107 1 210 4 gi|546918 orfY 3′ ofcomK [Bacillus subtilis, E26, Peptide Partial, 140 aa] 82 64 207pir|S43612|S43612 hypothetical protein Y - Bacillus subtilissp|P40398|YHXD_BACSU HYPOTHETICAL PROTEIN IN COMK 3′ REGION (ORFY)FRAGMENT). 4332 1 2 319 gi|42086 nitrate reductase alpha subunit[Escherichia coli] p|P09152|NARG_ECOLI 82 75 318 RESPIRATORY NITRATEREDUCTASE 1 ALPHA CHAIN (EC 7.99.4). (SUB 2-1247) 23 3 2574 1873gi|1199573 spsB [Sphingomonas sp.] 81 64 702 42 1 321 4 gi|466778 lysinespecific permease [Escherichia coli] 81 59 318 48 5 4051 4350 gi|1045937M. genitalium predicted coding region MG246 [Mycoplasma genitalium] 8162 300 51 4 1578 2579 pir|S16649|S166 dciAC protein - Bacillus subtilis81 55 1002 53 2 364 1494 gi|1303961 YqjJ [Bacillus subtilis] 81 67 113153 8 7971 6523 gi|146930 6-phosphogluconate dehydrogenase [Escherichiacoli] 81 66 1449 54 9 10119 9481 gi|143016 permease [Bacillus subtilis]81 65 639 54 10 11786 10212 gi|143015 gluconate kinase [Bacillussubtilis] 81 64 1575 57 17 13366 12749 pir|A25805|A258 L-lactatedehydrogenase (EC 1.1.1.27) - Bacillus subtilis 81 74 618 81 2 2217 1726gi|1222302 NifU-related protein [Haemophilus influenzae] 81 54 492 86 1374 3 gi|414017 ipa-93d gene product [Bacillus subtilis] 81 70 372 103 64861 3284 gi|971342 nitrate reductase beta subunit [Bacillus subtilis]sp|P42176|NARH_BACSU 81 64 1578 NITRATE REDUCTASE BETA CHAIN (EC1.7.99.4). 120 15 10845 12338 gi|1524392 GbsA [Bacillus subtilis] 81 671494 128 5 3676 4413 gi|143319 triose phosphate isomerase [Bacillusmegaterium] 81 64 738 131 9 9280 8252 gi|299163 alanine dehydrogenase[Bacillus subtilis] 81 68 1029 143 6 5471 4854 gi|439619 [Salmonellatyphimurium IS200 insertion sequence from SARA17, artial.], 81 61 618gene product [Salmonella typhimurium] 169 1 43 825 gi|897795 30Sribosomal protein [Pediococcus acidilactici] sp|P49668|RS2_PEDAC 30S 8165 783 RIBOSOMAL PROTEN S2. 230 1 226 2 gi|1125826 short region of weaksimilarity to tyrosine-protein kinase receptors in a 81 54 225fibronectin type III-like domain [Caenorhabditis elegans] 233 5 20002677 gi|467404 unknown [Bacillus subtilis] 81 63 678 241 2 2149 1217gi|16510 succinate - CoA ligase (GDP-forming) [Arabidopsis thaliana]ir|S30579|S30579 81 69 933 succinate—CoA ligase (GDP-forming) (EC6.2.1.4) pha chain - Arabidopsis thaliana (fragment) 256 1 1 981pir|S09411|S094 spoIIIE protein - [Bacillus subtilis] 81 65 981 259 32691 1630 sp|P28367|RF2_B PROBABLE PEPTIDE CHAIN RELEASE FACTOR 2 (RF-2)(FRAGMENT). 81 65 1062 275 2 1728 3581 gi|726480L-glutamine-n-fructose-6-phosphate amidotransferase [Bacillus subtilis]81 68 1854 285 1 735 4 gi|1204844 H. influenzae predicted coding regionHI0594 [Haemophilus influenzae] 81 63 732 296 1 99 1406 gi|467328adenylosuccinate synthetase [Bacillus subtilis] 81 67 1308 302 9 55905889 gi|147485 queA [Escherichia coli] 81 64 300 317 2 1137 1376gi|154961 resolvase [Transposon Tn917] 81 51 240 343 2 1034 1342gi|405955 yeeD [Escherichia coli] 81 60 309 360 2 1404 2471 gi|1204570aspartyl-tRNA synthetase [Haemophilus influenzae] 81 67 1068 364 5 57065161 gi|1204652 methylated-DNA-protein-cysteine methyltransferase[Haemophilus influenzae] 81 63 546 372 2 1135 563 gi|467416 unknown[Bacillus subtilis] 81 65 573 392 1 43 603 pir|S09411|S094 spoIIIEprotein - Bacillus subtilis 81 65 561 404 9 5252 6154 gi|606745 Bex[Bacillus subtilis] 81 65 903 426 2 1119 511 gi|39453 Manganesesuperoxide dismutase [Bacillus caldotenax] ir|S22053|S22053 81 66 609superoxide dismutase (EC 1.15.1.1) (Mn) - Bacillus ldotenax 480 7 56535889 pir|C37083|C370 hypothetical protein II (ompH 3′ region) -Salmonella typhimurium 81 57 237 [fragment] 625 3 1105 2070 gi|1262360protein kinase PknB [Mycobacterium leprae] 81 56 966 754 2 504 1064gi|1303902 YqhU [Bacillus subtilis] 81 71 561 842 1 86 430 gi|1405446transketolase [Bacillus subtilis] 81 68 345 953 1 400 2 gi|1205429dipeptide transport ATP-binding protein [Haemophilus influenzae] 81 57399 961 2 252 401 gi|487686 synergohymenotropic toxin [Staphylococcusintermedius] pir|S44944|S44944 81 72 150 synergohymenotropic toxin -Staphylococcus intermedius 1035 1 1 189 gi|1046138 M. genitaliumpredicted coding region MG423 [Mycoplasma genitalium] 81 43 189 1280 1449 228 gi|559164 helicase [Autographa californica nuclear polyhedrosisvirus] 81 43 222 sp|P24307|V143_NPVAC HELICASE. 3371 1 68 241 gi|1322245mevalonate pyrophosphate decarboxylase [Rattus norvegicus] 81 62 1743715 1 239 3 gi|537137 ORF_f388 [Escherichia coli] 81 58 237 3908 1 2325 gi|439619 [Salmonella typhimurium IS200 insertion sequence fromSARA17, artial.], 81 68 324 gene product [Salmonella typhimurium] 3940 13 401 gi|296464 ATPase [Lactococcus lactis] 81 69 399 3954 1 1 318gi|1224069 amidase [Moraxella catarrhalis] 81 68 318 4049 1 170 3gi|603768 HutI protein, imidazolone-5-propionate hydrolase [Bacillussubtilis] 81 68 168 gi|603768 HutI protein, imidazolone-5-propionatehydrolase Bacillus subtilis] 4209 1 1 324 gi|403373 glycerophosphoryldiester phosphodiesterase [Bacillus subtilis] 81 58 324pir|S37251|S37251 glycerophosphoryl diester phosphodiesterase - Bacillussubtilis 4371 1 322 17 gi|216677 indolepyruvate decarboxylase[Enterobacter cloacae] pir|S16013|S16013 81 72 306 indolepyruvatedecarboxylase (EC 4.1.1.—) - Enterobacter cloacae 4387 1 19 228gi|460689 TVG [Thermoactinomyces vulgaris] 81 59 210 4391 1 306 31gi|1524193 unknown [Mycobacterium tuberculosis] 81 67 276 4425 1 3 341gi|143015 gluconate kinase [Bacillus subtilis] 81 66 339 9 1 847 101gi|1064786 function unknown [Bacillus subtilis] 80 62 747 17 1 311 78gi|559164 helicase [Autographa californica nuclear polyhedrosis virus]80 40 234 sp|P24307|V143_NPVAC HELICASE. 45 2 1159 2448 gi|1109684 ProV[Bacillus subtilis] 80 63 1290 45 5 4032 4733 gi|1109687 ProZ [Bacillussubtilis] 80 55 702 54 8 9502 8738 gi|563952 gluconate permease[Bacillus licheniformis] 80 62 765 62 12 7545 6238 gi|854655 Na/Hantiporter system [Bacillus alcalophilus] 80 62 1308 62 14 8087 8683gi|559713 ORF [Homo sapiens] 80 68 597 67 16 13781 14122 gi|305002ORF_f356 [Escherichia coli] 80 65 342 70 13 10296 9097 gi|1303995 YqkN[Bacillus subtilis] 80 64 1200 98 9 6336 7130 gi|467428 unknown[Bacillus subtilis] 80 68 795 98 10 7294 7833 gi|467430 unknown[Bacillus subtilis] 80 64 540 98 11 7820 8737 gi|467431 high levelkasgamycin resistance [Bacillus subtilis] 80 61 918 109 16 14154 14813gi|580875 ipa-57d gene product [Bacillus subtilis] 80 63 660 112 1514294 16636 gi|1072361 pyruvate-formate-lyase [Clostridium pasteurianum]80 65 2343 139 1 726 4 gi|506699 CapC [Staphylococcus aureus] 80 58 723139 2 1448 717 gi|506698 CapB [Staphylococcus aureus] 80 59 732 174 42870 2469 gi|1146242 aspartate 1-decarboxylase [Bacillus subtilis] 80 61402 177 3 2102 2842 gi|467385 unknown [Bacillus subtilis] 80 70 741 1846 5912 5700 gi|161953 85-kDa surface antigen [Trypanosoma cruzi] 80 46213 186 4 3875 2382 gi|289282 glutamyl-tRNA synthetase [Bacillussubtilis] 80 65 1494 205 30 15140 14484 gi|40103 ribosomal protein L4[Bacillus stearothermophilus] 80 66 657 207 1 140 1315 gi|460259 enolase[Bacillus subtilis] 80 67 1176 211 3 1078 1590 gi|410131 ORFX7 [Bacillussubtilis] 80 61 513 235 2 1962 2255 gi|143797 valyl-tRNA synthetase[Bacillus stearothermophilus] sp|P11931|SYV_BACST 80 55 294 VALYL-TRNASYNTHETASE (EC 6.1.1.9) VALINE-TRNA LIGASE) (VALRS). 239 1 1 1263gi|143000 proton glutamate symport protein [Bacillus stearothermophilus]80 59 1263 pir|S26247|S26247 glutamate/aspartate transport protein -Bacillus stearothermophilus 272 5 2461 2198 gi|709993 hypotheticalprotein [Bacillus subtilis] 80 54 264 301 3 1111 776 gi|467418 unknown[Bacillus subtilis] 80 58 336 310 4 4501 3305 gi|1177686 acuC geneproduct [Staphylococcus xylosus] 80 67 1197 310 6 5258 7006 gi|348053acetyl-CoA synthetase [Bacillus subtilis] 80 67 1749 310 7 7410 9113gi|1103865 formyl-tetrahydrofolate synthetase [Streptococcus mutans] 8067 1704 325 3 1114 1389 gi|310325 outer capsid protein [Rotavirus sp.]80 40 276 337 1 636 4 gi|537049 ORF_o470 [Escherichia coli] 80 55 633374 2 929 1228 gi|1405448 YneF [Bacillus subtilis] 80 70 300 375 5 30623331 gi|467448 unknown [Bacillus subtilis] 80 68 270 388 1 267 587gi|1064791 function unknown [Bacillus subtilis] 80 65 321 394 1 9 659gi|304976 matches PS00017: ATP_GTP_A and PS00301: EFACTOR_GTP; similarto longation 80 65 651 factor G, TetM/Tet0 tetracycline-resistanceproteins Escherichia coli] 456 1 625 1263 gi|1146183 putative [Bacillussubtilis] 80 65 639 475 1 1 654 gi|288269 beta-fructofuranosidase[Staphylococcus xylosus] 80 66 654 544 2 1449 2240 gi|529754 speC[Streptococcus pyogenes] 80 50 792 622 4 1623 1871 gi|1483545 unknown[Mycobacterium tuberculosis] 80 65 249 719 1 1 1257 gi|1064791 functionunknown [Bacillus subtilis] 80 68 1257 739 1 107 838 gi|666983 putativeATP binding subunit [Bacillus subtilis] 80 61 732 745 2 414 247gi|1511600 coenzyme PQQ synthesis protein III [Methanococcus jannaschii]80 61 168 822 1 17 679 gi|410141 ORFX17 [Bacillus subtilis] 80 68 663827 2 836 681 gi|1205301 leukotoxin secretion ATP-binding protein[Haemophilus influenzae] 80 54 156 1044 1 3 149 gi|60632 vp2 [Marburgvirus] 80 55 147 1220 2 413 255 pir|A61072|EPSG gallidermin precursor -Staphylococcus gallinarum 80 74 159 2519 1 75 275 gi|147556 dpj[Escherichia coli] 80 45 201 2947 1 279 55 gi|1184680 polynucleotidephosphorylase [Bacillus subtilis] 80 62 225 3120 1 2 226 gi|517205 67kDa Myosin-crossreactive streptococcal antigen [Streptococcus yogenes]80 65 225 3191 1 148 2 gi|151259 HMG-CoA reductase (EC 1.1.1.88)[Pseudomonas mevalonii] pir|A44756|A44756 80 59 147hydroxymethylglutaryl-CoA reductase (EC 1.1.1.88) Pseudomonas sp. 3560 2285 434 gi|217130 photosystem I core protein B [Synechococcus vulcanus]80 70 150 3655 1 47 346 gi|415855 deoxyribose aldolase [Mycoplasmahominis] 80 56 300 3658 2 324 584 gi|551531 2-nitropropane dioxygenase[Williopsis saturnus] 80 54 261 3769 1 400 2 gi|1339950 large subunit ofNADH-dependent glutamate synthase [Plectonema boryanum] 80 68 399 3781 1348 4 gi|166412 NADH-glutamate synthase [Medicago sativa] 80 62 345 39881 48 287 gi|1204696 fructose-permease IIBC component [Haemophilusinfluenzae] 80 69 240 4030 1 287 3 gi|1009366 Respiratory nitratereductase [Bacillus subtilis] 80 60 285 4092 1 275 3 gi|1370207 orf6[Lactobacillus sake] 80 69 273 4103 1 342 4 gi|39956 IIGlc [Bacillussubtilis] 80 65 339 4231 1 348 4 gi|289287 UDP-glucose pyrophosphorylase[Bacillus subtilis] 80 65 345 4265 1 299 3 gi|603768 HutI protein,imidazolone-5-propionate hydrolase [Bacillus subtilis] 80 63 297gi|603768 HutI protein, imidazolone-5-propionate hydrolase Bacillussubtilis] 4504 1 250 2 gi|1339950 large subunit of NADH-dependentglutamate synthase [Plectonema boryanum] 80 68 249 2 6 5998 6798gi|535351 codY [Bacillus subtilis] 79 63 801 4 7 7051 5807 gi|603768HutI protein, imidazolone-5-propionate hydrolase [Bacillus subtilis] 7964 1245 gi|603768 HutI protein, imidazolone-5-propionate hydrolaseBacillus subtilis] 25 6 5273 5515 pir|A36728|A367 acyl carrier protein -Rhizobium meliloti 79 65 243 59 2 1173 1424 gi|147923 threoninedehydratase 2 (EC 4.2.1.16) [Escherichia coli] 79 75 252 60 1 1 204gi|666115 orf1 upstream of glucose kinase [Staphylococcusxylosus]pir|S52351|S52351 79 60 204 hypothetical protein 1 -Staphylococcus xylosus 81 1 1590 178 gi|466882 pps1; B1496_C2_189[Mycobacterium leprae] 79 64 1413 85 7 6505 5987 gi|143364phosphoribosyl aminoimidazole carboxylase I (PUR-E) [Bacillus subtilis]79 60 519 89 6 4554 3448 gi|144906 product homologous to E. colithioredoxin reductase: J. Biol. Chem. 1988) 79 35 1107 263: 9015-9019,and to F52a protein of alkyl hydroperoxide eductase from S. typhimurium:J.Biol.Chem. (1990) 265: 10535-10540; pen reading frame A [Clostridiumpasteurianum] 102 11 7489 8571 gi|143093 ketol-acid reductoisomerase[Bacillus subtilis] sp|P37253|ILVC_BACSU KETOL- 79 64 1083 ACIDREDUCTOISOMERASE (EC 1.1.1.86) ACETOHYDROXY-ACID ISOMEROREDUCTASE)(ALPHA-KETO-BETA-HYDROXYLACIL EDUCTOISOMERASE). 102 14 11190 12563gi|149428 putative [Lactococcus lactis] 79 65 1374 127 9 7792 9372gi|458688 PrfC/RF3 [Dichelobacter nodosus] 79 68 1581 139 3 1983 1426gi|506697 CapA [Staphylococcus aureus] 79 55 558 144 2 1156 668gi|1498296 peptide methionine sulfoxide reductase [Streptococcuspneumoniae] 79 47 489 148 2 529 1098 gi|467457 hypoxanthine-guaninephosphoribosyltransferase [Bacillus subtilis] 79 59 570 gi|467457hypoxanthine-guanine phosphoribosyltransferase [Bacillus subtilis] 150 1591 217 gi|755602 unknown [Bacillus subtilis] 79 61 375 176 1 587 135gi|297874 fructose-bisphosphate aldolase [Staphylococcus carnosus]pir|A49943|A49943 79 65 453 fructose-bisphosphate aldolase (EC4.1.2.13) - Staphylococcus carnosus (strain TM300) 186 7 6874 6164gi|1314298 ORF5; putative Sms protein; similar to Sms proteins fromHaemophilus 79 64 711 influenzae and Escherichia coli [Listeriamonocytogenes] 205 16 8498 8109 gi|1044980 ribosomal protein L18[Bacillus subtilis] 79 70 390 211 1 1 519 gi|1303994 YqkM [Bacillussubtilis] 79 62 519 223 2 2801 1419 gi|488430 alcohol dehydrogenase 2[Entamoeba histolytica] 79 60 1383 243 8 7896 6877 gi|580883 ipa-88dgene product [Bacillus subtilis] 79 60 1020 279 4 3721 4329 gi|413930ipa-6d gene product [Bacillus subtilis] 79 59 609 300 1 11 1393gi|403372 glycerol 3-phosphate permease [Bacillus subtilis] 79 62 1383307 3 1935 940 gi|950062 hypothetical yeast protein 1 [Mycoplasmacapricolum] pir|S48578|S48578 79 60 996 hypothetical protein -Mycoplasma capricolum SGC3) (fragment) 352 6 8886 7666 gi|216854 P47K[Pseudomonas chlororaphis] 79 59 1221 412 1 578 3 gi|143177 putative[Bacillus subtilis] 79 51 576 481 3 621 1124 gi|786163 Ribosomal ProteinL10 [Bacillus subtilis] 79 66 504 516 1 352 2 gi|805090 NisF[Lactococcus lactis] 79 48 351 525 2 1426 395 gi|143371 phosphoribosylaminoimidazole synthetase (PUR-M) [Bacillus subtilis] 79 61 1032pir|H29326|AJBSCL phosphoribosylformylglycinamidine cyclo-ligase EC6.3.3.1) - Bacillus subtilis 538 4 2825 2202 gi|1370207 orf6[Lactobacillus sake] 79 67 624 570 1 2 421 gi|476160 arginine permeasesubstrate-binding subunit [Listeria monocytogenes] 79 61 420 645 8 26633241 gi|153898 transport protein [Salmonella typhimurium] 79 62 579 6831 75 374 gi|1064795 function unknown [Bacillus subtilis] 79 62 300 816 33987 3274 gi|1407784 orf-1; novel antigen [Staphylococcus aureus] 79 62714 2929 1 3 401 gi|1524397 glycine betaine transporter OpuD [Bacillussubtilis] 79 61 399 2937 1 202 47 pir|S52915|S529 nitrate reductasealpha chain - Bacillus subtilis (fragment) 79 58 156 2940 1 385 2gi|149429 putative [Lactococcus lactis] 79 72 384 2946 1 286 2 gi|1432672-oxoglutarate dehydrogenase (odhA; EC 1.2.4.2) [Bacillus subtilis] 7961 285 2999 1 3 212 gi|710020 nitrite reductase (nirB) [Bacillussubtilis] 79 59 210 3022 1 332 150 gi|450686 3-phosphoglycerate kinase[Thermotoga maritima] 79 61 183 3064 1 3 314 gi|1204436 pyruvateformate-lyase [Haemophilus influenzae] 79 60 312 3083 1 2 220 gi|1149662hypD gene product [Clostridium perfringens] 79 56 219 3126 1 411 121gi|1339950 large subunit of NADH-dependent glutamate synthase[Plectonema boryanum] 79 55 291 3181 1 326 45 gi|1339950 large subunitof NADH-dependent glutamate synthase [Plectonema boryanum] 79 59 2823345 1 3 476 gi|871784 Clp-like ATP-dependent protease binding subunit[Bos taurus] 79 63 474 3718 1 270 4 pir|C36889|C368 leuB protein,inactive - Lactococcus lactis subsp. lactis (strain IL1403) 79 71 2673724 2 159 401 gi|1009366 Respiratory nitrate reductase [Bacillussubtilis] 79 64 243 3836 1 312 16 gi|1524193 unknown [Mycobacteriumtuberculosis] 79 65 297 3941 1 2 334 gi|415855 deoxyribose aldolase[Mycoplasma hominis] 79 54 333 4113 1 3 341 gi|143015 gluconate kinase[Bacillus subtilis] 79 63 339 4501 1 209 12 gi|1022726 unknown[Staphylococcus haemolyticus] 79 66 198 4612 1 2 238 gi|460689 TVG[Thermoactinomyces vulgaris] 79 58 237 2 1 2 1213 gi|520753 DNAtopoisomerase I [Bacillus subtilis] 78 64 1212 8 2 1220 174 gi|216151DNA polymerase (gene L; ttg start codon) [Bacteriophage SP02] gi|57919778 72 1047 SP02 DNA polymerase (aa 1-648) [Bacteriophage SP02]pir|A21498|DJBPS2 DNA- directed DNA polymerase (EC 2.7.7.7) - phage P029 2 1089 838 gi|1064787 function unknown [Bacillus subtilis] 78 57 25232 8 6803 7702 gi|146974 NH3-dependent NAD synthetase [Escherichia coli]78 63 900 36 4 2941 3138 gi|290503 glutamate permease [Escherichia coli]78 53 198 53 15 16221 14758 gi|1303941 YqiV [Bacillus subtilis] 78 581464 57 14 10520 12067 gi|1072418 glcA gene product [Staphylococcuscarnosus] 78 65 1548 66 7 5812 4826 gi|1212729 YqhJ [Bacillus subtilis]78 67 987 67 4 4029 4376 gi|466612 nikA [Escherichia coli] 78 71 348 919 10058 10942 gi|467380 stage 0 sporultion [Bacillus subtilis] 78 50 885102 12 8574 10130 gi|149426 putative [Lactococcus lactis] 78 61 1557 1126 3540 4463 gi|854234 cymG gene product [Klebsiella oxytoca] 78 56 924124 2 1061 234 gi|405622 unknown [Bacillus subtilis] 78 60 828 130 31805 2260 gi|1256636 putative [Bacillus subtilis] 78 71 456 133 1 377 3gi|168060 lamB [Emericella nidulans] 78 59 375 166 4 6163 5201 gi|451216Mannosephosphate Isomerase [Streptococcus mutans] 78 63 963 186 1 795 4gi|289284 cysteinyl-tRNA synthetase [Bacillus subtilis] 78 63 792 195 42315 1881 gi|1353874 unknown [Rhodobacter capsulatus] 78 58 435 199 33623 2967 gi|143525 succinate dehydrogenase cytochrome b-558 subunit[Bacillus subtilis] 78 57 657 pir|A29843|DEBSSC succinate dehydrogenase(EC 1.3.99.1) cytochrome 558 - Bacillus subtilis 199 4 5557 3905gi|142521 deoxyribodipyrimidine photolyase [Bacillus subtilis]pir|A37192|A37192 uvrB 78 62 1653 protein - Bacillus subtilissp|P14951|UVRC_BACSU EXCINUCLEASE ABC SUBUNIT C. 223 3 3523 3215gi|439596 [Escherichia coli IS200 insertion sequence from ECOR63,partial.), ene 78 47 309 product [Escherichia coli] 299 4 1865 2149gi|467439 temperature sensitive cell division [Bacillus subtilis] 78 62285 321 9 7315 6896 gi|142979 ORF3 is homologous to an ORF downstream ofthe spoT gene of E. coli; RF3 78 55 420 [Bacillus stearothermophilus]352 4 3714 3944 gi|349050 actin 1 [Pneumocystis carinii] 78 42 231 352 56093 4594 gi|903587 NADH dehydrogenase subunit 5 [Bacillus subtilis]sp|P39755|NDHF_BACSU NADH 78 58 1500 DEHYDROGENASE SUBUNIT 5 (EC1.6.5.3) NADH-UBIQUINONE OXIDOREDUCTASE CHAIN 5). 376 1 2 583 gi|551693dethiobiotin synthase [Bacillus sphaericus] 78 34 582 424 2 1595 1768gi|1524117 alpha-acetolactate decarboxylase [Lactococcus lactis] 78 68174 450 1 988 62 gi|1030068 NAD(P)H oxidoreductase, isoflavone reductasehomologue [Solanum tuberosum] 78 63 927 558 1 562 362 gi|1511588bifunctional protein [Methanococcus jannaschii] 78 60 201 670 3 11521589 gi|1122759 unknown [Bacillus subtilis] 78 64 438 714 1 64 732gi|143460 37 kd minor sigma factor (rpoF, sigB; ttg start codon)[Bacillus subtilis] 78 57 669 814 1 3 368 gi|1377833 unknown [Bacillussubtilis] 78 59 366 981 1 692 3 gi|143802 GerC2 [Bacillus subtilis] 7864 690 995 2 727 476 gi|296947 uridine kinase [Escherichia coli] 78 64252 1045 1 3 401 gi|1407784 orf-1; novel antigen [Staphylococcus aureus]78 61 399 1163 2 186 4 gi|410117 diaminopimelate decarboxylase [Bacillussubtilis] 78 54 183 2191 1 399 4 gi|215098 excisionase [Bacteriophage154a] 78 65 396 2933 1 2 181 gi|1204436 pyruvate formate-lyase[Haemophilus influenzae] 78 73 180 3041 2 129 317 gi|624632 GltL[Escherichia coli] 78 53 189 3581 1 105 401 gi|763186 3-ketoacyl-coAthiolase [Saccharomyces cerevisiae] 78 55 297 3709 1 3 230 gi|460689 TVG[Thermoactinomyces vulgaris] 78 58 228 3974 1 265 2 gi|558839 unknown[Bacillus subtilis] 78 65 264 3980 1 3 401 gi|39956 IIGlc [Bacillussubtilis] 78 62 399 4056 1 354 61 gi|1256635 dihydroxy-acid dehydratase[Bacillus subtilis] 78 55 294 4114 1 316 2 pir|S09372|S093 hypotheticalprotein - Trypanosoma brucei 78 62 315 4185 1 3 179 gi|1339950 largesubunit of NADH-dependent glutamate synthase [Plectonema boryanum] 78 58177 4235 1 329 3 gi|558839 unknown [Bacillus subtilis] 78 60 327 4352 1302 63 gi|603768 HutI protein, imidazolone-5-propionate hydrolase[Bacillus subtilis] 78 63 240 gi|603768 HutI protein,imidazolone-5-propionate hydrolase Bacillus subtilis] 4368 1 307 2gi|1353678 heavy-metal transporting P-type ATPase [Proteus mirabilis] 7859 306 4461 1 216 4 gi|1276841 glutamate synthase (GOGAT) [Porphyrapurpurea] 78 36 213 4530 1 238 2 gi|39956 IIGlc [Bacillus subtilis] 7865 237 3 2 2073 1177 gi|1109684 ProV [Bacillus subtilis] 77 56 897 12 21965 1504 gi|467335 ribosomal protein L9 [Bacillus subtilis] 77 59 46227 1 2 388 gi|1212728 YqhI [Bacillus subtilis] 77 63 387 39 2 590 1252gi|40054 phenylalanyl-tRNA synthetase beta subunit (AA 1-804) [Bacillussubtilis] 77 60 663 42 6 2704 2931 gi|606241 30S ribosomal subunitprotein S14 [Escherichia coli] sp|P02370|RS14_ECOLI 77 65 228 30SRIBOSOMAL PROTEIN S14. (SUB 2-101) 46 18 15459 16622 gi|297798mitochondrial formate dehydrogenase precursor [Solanum tuberosum] 77 551164 pir|JQ2272|JQ2272 formate dehydrogenase (EC 1.2.1.2) precursor,itochondrial - potato 100 4 4002 3442 gi|1340128 ORF1 [Staphylococcusaureus] 77 54 561 102 8 5378 5713 gi|1311482 acetolactate synthase[Thermus aquaticus] 77 57 336 109 7 4742 5383 gi|710637 Unknown[Bacillus subtilis] 77 56 642 117 1 2 1228 gi|1237015 ORF4 [Bacillussubtilis] 77 53 1227 124 10 7688 7053 gi|405819 thymidine kinase[Bacillus subtilis] 77 63 636 147 3 985 824 gi|849027 hypothetical15.9-kDa protein [Bacillus subtilis] 77 37 162 152 10 7354 7953gi|1205583 spermidine/putrescine transport ATP-binding protein[Haemophilus 77 55 600 influenzae] 169 2 1004 1282 gi|473825 ‘elongationfactor EF-Ts’ [Escherichia coli] 77 58 279 184 2 380 1147 gi|216314esterase [Bacillus stearothermophilus] 77 60 768 189 7 3296 3868gi|853809 ORF3 [Clostridium perfringens] 77 48 573 193 1 132 290gi|1303788 YqeH [Bacillus subtilis] 77 54 159 195 8 8414 8088 gi|1499620M. jannaschii predicted coding region MJ0798 [Methanococcus jannaschii]77 44 327 205 8 5204 4980 gi|216340 ORF for adenylate kinase [Bacillussubtilis] 77 61 225 205 29 14502 14209 gi|786155 Ribosomal Protein L23[Bacillus subtilis] 77 62 294 211 5 1908 2084 gi|410132 ORFX8 [Bacillussubtilis] 77 47 177 217 5 3478 4416 gi|496254fibronectin/fibrinogen-binding protein [Streptococcus pyogenes] 77 54939 232 1 267 998 gi|1407784 orf-1; novel antigen [Staphylococcusaureus] 77 57 732 233 2 1346 873 gi|467408 unknown [Bacillus subtilis]77 61 474 243 3 2299 1937 gi|516155 unconventional myosin [Sus scrofa]77 32 363 299 1 68 769 gi|467436 unknown [Bacillus subtilis] 77 54 702301 4 1283 1098 gi|950071 ATP-bind. pyrimidine kinase [Mycoplasmacapricolum] pir|S48605|S48605 77 48 186 hypothetical protein -Mycoplasma capricolum SGC3) (fragment) 302 5 2741 3211 gi|508980 pheB[Bacillus subtilis] 77 57 471 302 7 3835 4863 gi|147783 ruvB protein[Escherichia coli] 77 60 1029 307 9 4797 4192 gi|1070015protein-dependent [Bacillus subtilis] 77 60 606 312 1 99 1391 gi|143165malic enzyme (EC 1.1.1.38) [Bacillus stearothermophilus]pir|A33307|DEBSXS 77 62 1293 malate dehydrogenaseoxaloacetate-decarboxylating) (EC 1.1.1.38) - Bacillus tearothermophilus312 2 1541 2443 gi|1399855 carboxyltransferase beta subunit[Synechococcus PCC7942] 77 58 903 321 5 4596 3526 gi|39844 fumarase(citG) (aa 1-462) [Bacillus subtilis] 77 65 1071 354 1 47 568 gi|1154634YmaB [Bacillus subtilis] 77 57 522 365 1 2 1021 gi|143374 phosphoribosylglycinamide synthetase (PUR-D; gtg start codon) Bacillus 77 62 1020subtilis] 374 1 1 708 gi|1405446 transketolase [Bacillus subtilis] 77 61708 385 1 565 2 gi|533099 endonuclease III [Bacillus subtilis] 77 63 564392 2 594 1940 gi|556014 UDP-N-acetyl muramate-alanine ligase [Bacillussubtilis] 77 65 1347 sp|P40778|MURC_BACSU UDP-N-ACETYLMURAMATE-ALANINELIGASE (EC .3.2.8) (UDP-N-ACETYLMURANOYL-L-ALANINE SYNTHETASE)(FRAGMENT). 405 5 3570 3061 gi|1303912 YqhW [Bacillus subtilis] 77 64510 487 4 1302 1472 gi|432427 ORF1 gene product (Acinetobactercalcoaceticus) 77 48 171 522 1 2 562 pir|A01179|SYBS tyrosine-tRNAligase (EC 6.1.1.1) - Bacillus stearothermophilus 77 63 561 523 2 13511115 gi|1387979 44% identity over 302 residues with hypothetical proteinfrom Synechocystis 77 48 237 sp, accession D64006_CD; expression inducedby environmental stress; some similarity to glycosyl transferases; twopotential membrane-spanning helices [Bacillus subtil 536 2 612 241gi|143366 adenylosuccinate lyase (PUR-B) [Bacillus subtilis]pir|C29326|WZBSDS 77 61 372 adenylosuccinate lyase (EC 4.3.2.2) -Bacillus subtilis 548 2 339 872 gi|143387 aspartate transcarbamylase[Bacillus subtilis] 77 56 534 597 1 2 481 gi|904198 hypothetical protein[Bacillus subtilis] 77 33 480 633 2 1313 879 gi|387577 ORF1A [Bacillussubtilis] 77 64 435 642 1 85 360 gi|46971 epiP gene product[Staphylococcus epidermidis] 77 61 276 659 1 125 1219 gi|1072381glutamyl-aminopeptidase [Lactococcus lactis] 77 62 1095 670 4 1587 1820gi|1122760 unknown [Bacillus subtilis] 77 58 234 789 1 2 391 gi|1377823aminopeptidase [Bacillus subtilis] 77 65 390 815 1 10 573 gi|1303861YqgN [Bacillus subtilis] 77 49 564 899 1 1 225 gi|1204844 H. influenzaepredicted coding region HI0594 [Haemophilus influenzae] 77 55 225 1083 13 188 gi|460828 B969 [Saccharomyces cerevisiae] 77 66 186 1942 1 209 3gi|160047 p101/acidic basic repeat antigen [Plasmodium falciparum]pir|A29232|A29232 77 38 207 101 K malaria antigen precursor - Plasmodiumalciparum (strain Camp) 2559 1 1 171 gi|1499034 M. jannaschii predictedcoding region MJ0255 [Methanococcus jannaschii] 77 61 171 2933 2 243 401gi|42370 pyruvate formate-lyase (AA 1-760) [Escherichia coli]ir|S01788|S01788 77 72 159 formate C-acetyltransferase (EC 2.3.1.54) -Echerichia coli 2966 1 56 292 gi|1524397 glycine betaine transporterOpuD [Bacillus subtilis] 77 45 237 2976 1 309 4 gi|40003 oxoglutaratedehydrogenase (NADP+) [Bacillus subtilis] p|P23129|ODO1_BACSU 77 60 3062-OXOGLUTARATE DEHYDROGENASE E1 COMPONENT (EC 2.4.2)(ALPHA-KETOGLUTARATE DEHYDROGENASE). 2979 2 400 122 gi|1204354 sporegermination and vegetative growth protein [Haemophilus influenzae] 77 61279 2988 1 377 153 gi|438465 Probable operon with orfF. Possiblealternative initiation codon, ases 77 55 225 2151-2153. Homology withacetyltransferases.; putative Bacillus subtilis] 2990 1 167 3 gi|142562ATP synthase epsilon subunit [Bacillus megaterium] pir|B28599|PWBSEM H+−77 63 165 transporting ATP synthase (EC 3.6.1.34) psilon chain -Bacillus megaterium 3032 1 3 389 gi|488430 alcohol dehydrogenase 2[Entamoeba histolytica] 77 56 387 3057 1 1 195 gi|468764 mocR geneproduct (Rhizobium meliloti) 77 50 195 4008 1 400 74 gi|603768 HutIprotein, imidazolone-5-propionate hydrolase [Bacillus subtilis] 77 52327 gi|603768 HutI protein, imidazolone-5-propionate hydrolase Bacillussubtilis] 4048 1 386 69 gi|216278 gramicidin S synthetase 1 [Bacillusbrevis] 77 55 318 4110 1 3 368 pir|S52915|S529 nitrate reductase alphachain - Bacillus subtilis (fragment) 77 61 366 4115 1 1 348 gi|517205 67kDa Myosin-crossreactive streptococcal antigen [Streptococcus yogenes]77 65 348 4225 1 297 4 gi|1322245 mevalonate pyrophosphate decarboxylase[Rattus norvegicus] 77 60 294 4611 2 327 160 gi|508979 GTP-bindingprotein [Bacillus subtilis] 77 57 168 4668 1 182 3 pir|S52915|S529nitrate reductase alpha chain - Bacillus subtilis (fragment) 77 61 18025 1 2 1627 gi|1150620 MmsA [Streptococcus pneumoniae] 76 58 1626 38 51488 2537 pir|A43577|A435 regulatory protein pfoR - Clostridiumperfringens 76 57 1050 52 5 2962 4041 gi|1161061 dioxygenase[Methylobacterium extorquens] 76 62 1080 56 20 27389 27955 gi|467402unknown [Bacillus subtilis] 76 56 567 57 15 12046 12219 gi|1206040 weaksimilarity to keratin [Caenorhabditis elegans] 76 40 174 91 2 1062 2261gi|475715 acetyl coenzyme A acetyltransferase (thiolase) [Clostridiumcetobutylicum] 76 57 1200 98 2 818 1624 gi|467422 unknown [Bacillussubtilis] 76 62 807 98 5 2965 3228 gi|897793 y98 gene product[Pediococcus acidilactici] 76 52 264 98 8 5922 6326 gi|467427methionyl-tRNA synthetase [Bacillus subtilis] 76 53 405 104 3 1322 1885gi|216151 DNA polymerase (gene L; ttg start codon) [Bacteriophage SPO2]gi|579197 76 63 564 SPO2 DNA polymerase (aa 1-648) [Bacteriophage SPO2)pir|A21498|DJBPS2 DNA- directed DNA polymerase (EC 2.7.7.7) - phage PO2124 9 7055 5976 gi|853776 peptide chain release factor 1 [Bacillussubtilis] pir|S55437|S55437 76 58 1080 peptide chain release factor 1 -Bacillus subtilis 164 5 2832 3311 gi|1204976 prolyl-tRNA synthetase[Haemophilus influenzae] 76 53 480 168 2 1841 1065 gi|1177253 putativeATP-binding protein of ABC-type [Bacillus subtilis] 76 58 777 189 2 163888 gi|467384 unknown [Bacillus subtilis] 76 63 726 235 3 2253 3518gi|142936 folyl-polyglutamate synthetase [Bacillus subtilis]pir|B40646|B40646 folC - 76 53 1266 Bacillus subtilis 236 1 335 925gi|1146197 putative [Bacillus subtilis] 76 54 591 237 8 5323 5541gi|1279261 F13G3.6 [Caenorhabditis elegans] 76 47 219 263 5 4585 3680gi|1510348 dihydrodipicolinate synthase [Methanococcus jannaschii] 76 49906 304 3 1051 1794 gi|666982 putative membrane spanning subunit[Bacillus subtilis]pir|S52382|S52382 76 60 744 probable membranespanning protein - Bacillus subtilis 312 4 3611 4624 gi|1433126-phospho-1-fructokinase (gtg start codon; EC 2.7.1.11) [Bacillus 76 561014 tearothermophilus) 343 1 2 1036 gi|405956 yeeE [Escherichia coli]76 59 1035 347 1 409 1701 gi|396304 acetylornithine deacetylase[Escherichia coli] 76 72 1293 358 1 672 1907 gi|1146215 39.0% identityto the Escherichia coli S1 ribosomal protein; putative 76 58 1236[Bacillus subtilis] 371 1 1 222 gi|537084 alternate gene name mgt; CGSite No. 497 [Escherichia coli] 76 61 222 pir|S56468|S56468 mgtAprotein - Escherichia coli 379 4 4331 4858 gi|143268 dihydrolipoamidetranssuccinylase (odhB; EC 2.3.1.61) [Bacillus subtilis] 76 61 528 404 54022 4492 gi|1303823 YqfG [Bacillus subtilis] 76 60 471 411 1 2 307gi|486025 ORF YKL027w [Saccharomyces cerevisiae] 76 55 306 472 3 28541352 gi|1405464 AlsT [Bacillus subtilis] 76 57 1503 546 1 273 995gi|153821 streptococcal pyrogenic exotoxin type C (speC) precursorStreptococcus 76 36 723 pyogenes] 588 1 557 60 gi|1002520 MutS [Bacillussubtilis] 76 61 498 591 1 16 735 gi|885934 ClpB [Synechococcus sp.] 7644 720 602 2 175 798 gi|1486422 OppD homologue [Rhizobium sp.] 76 52 624619 2 290 33 gi|330613 major capsid protein [Human cytomegalovirus] 7647 258 660 4 2568 3302 gi|904199 hypothetical protein [Bacillussubtilis] 76 55 735 677 1 228 4 gi|40177 spoOF gene product [Bacillussubtilis] 76 58 225 962 1 24 206 gi|142443 adenylosuccinate synthetase[Bacillus subtilis]sp|P29726|PURA_BACSU 76 67 183 ADENYLOSUCCINATESYNTHETASE (EC 6.3.4.4) IMP —ASPARTATE LIGASE). 978 1 580 2 gi|1511333M. jannaschii predicted coding region MJ1322 [Methanococcus jannaschii]76 56 579 997 1 244 2 gi|467154 No definition line found [Mycobacteriumleprae] 76 38 243 1563 1 266 3 gi|1303984 YqkG [Bacillus subtilis] 76 52264 2184 1 182 3 gi|506706 CapJ [Staphylococcus aureus] 76 38 180 2572 11 387 gi|153898 transport protein [Salmonella typhimurium] 76 65 3872942 1 29 400 gi|710020 nitrite reductase (nirB) [Bacillus subtilis] 7659 372 2957 1 216 55 gi|1511251 hypothetical protein (SP: P42404)[Methanococcus janneschii] 76 47 162 2980 1 279 4 gi|1405464 AlsT[Bacillus subtilis] 76 53 276 3015 1 326 3 gi|408115 ornithineacetyltransferase [Bacillus subtilis] 76 61 324 3124 1 13 174 gi|882705ORF_o401 (Escherichia coli) 76 65 162 3179 1 3 161 gi|168477ferredoxin-dependent glutamate synthase [Zea mays]pir|A38596|A38596 7653 159 glutamate synthase (ferredoxin) (EC 1.4.7.1)- maize 3789 1 2 379gi|39956 IIGlc [Bacillus subtilis) 76 55 378 3892 1 3 314 gi|1510398ferripyochelin binding protein [Methanococcus jannaschii] 76 52 312 39281 400 2 gi|143016 permease [Bacillus subtilis] 76 59 399 4159 1 386 15sp|P80544|MRSP_(—) METHICILLIN-RESISTANT SURFACE PROTEIN (FRAGMENTS) 7666 372 4204 1 17 331 gi|29646 ATPase [Lactococcus lactis] 76 56 315 43981 249 4 gi|987255 Menkes disease gene [Homo sapiens] 76 48 246 4506 1 2313 gi|216746 (D-lactate dehydrogenase [Lactobacillus plantarum] 76 47312 4546 1 247 17 gi|1339950 large subunit of NADH-dependent glutamatesynthase [Plectonema boryanum] 76 61 231 4596 1 191 3 gi|560027cellulose synthase [Acetobacter xylinum] 76 70 189 4 5 4337 3417gi|882532 ORF_o294 [Escherichia coli] 75 59 921 6 1 164 952 gi|40960OTCase [Escherichia coli] 75 56 789 12 3 3944 1953 gi|467336 unknown[Bacillus subtilis] 75 57 1992 23 18 17310 16348 gi|12964330-acetylserine sulfhydrylase B [Alcaligenes eutrophus] 75 55 963 25 32356 3393 gi|1502419 PlsX [Bacillus subtilis] 75 56 1038 36 8 5765 6037gi|1256517 unknown [Schizosaccharomyces pombe] 75 45 273 46 13 1118612058 gi|48972 nitrate transporter [Synechococcus sp.] 75 46 873 51 73474 3677 gi|143607 sporulation protein [Bacillus subtilis] 75 61 204 5316 16590 16330 gi|143402 (recombination protein (ttg start codon)[Bacillus subtilis] gi|1303923 RecN 75 51 261 [Bacillus subtilis] 74 32568 1564 gi|1204847 ornithine carbamoyltransferase [Haemophilusinfluenzae] 75 61 1005 85 3 3930 3232 gi|143368 phosphoribosylformylglycinamidine synthetase I (PUR-L; gtg start odon) 75 63 699 [Bacillussubtilis] 85 5 4878 4168 gi|143367 phosphoribosyl aminoidazolesuccinocarboxamide synthetase (PUR-C; tg start 75 55 711 codon)[Bacillus subtilis] 85 8 6625 7530 gi|1303916 YqiA [Bacillus subtilis]75 53 906 87 3 2340 3590 gi|1064813 homologous to sp: PHOR_BACSU[Bacillus subtilis] 75 56 1251 87 6 6084 6896 gi|1064810 functionunknown [Bacillus subtilis] 75 61 813 108 2 1503 1162 gi|1001824hypothetical protein [Synechocystis sp.] 75 51 342 110 3 1748 3727gi|1147593 putative ppGpp synthetase [Streptomyces coelicolor] 75 551980 110 7 4353 5252 gi|1177251 clwD gene product [Bacillus subtilis] 7575 900 120 14 10649 10032 gi|1524394 ORF-2 upstream of gbsAB operon[Bacillus subtilis] 75 55 618 121 5 2050 4221 gi|1154632 NrdE [Bacillussubtilis] 75 54 2172 124 1 143 3 gi|405622 unknown [Bacillus subtilis]75 56 141 128 1 81 1139 gi|143316 (gap) gene products [Bacillusmegaterium] 75 48 1059 130 8 5760 5903 gi|1256654 54.8% identity withNeisseria gonorrhoeae regulatory protein PilB; putative 75 62 144[Bacillus subtilis] 136 2 3185 1890 gi|467403 seryl-tRNA synthetase[Bacillus subtilis] 75 54 1296 161 10 5439 5798 gi|1001195 hypotheticalprotein [Synechocystis sp.] 75 55 360 172 4 2995 2171 gi|755153ATP-binding protein [Bacillus subtilis] 75 52 825 179 1 1107 190gi|143037 porphobilinogen deaminase [Bacillus subtilis] 75 58 918 195 109374 9219 sp|P25745|YCFB_(—) HYPOTHETICAL PROTEIN IN PURB 5′ REGION(ORF-15) (FRAGMENT) 75 60 156 200 4 2605 4596 gi|142440 ATP-dependentnuclease [Bacillus subtilis] 75 56 1992 206 3 5620 4340 gi|1256135 YbbF[Bacillus subtilis] 75 53 1281 216 2 159 389 gi|1052800 unknown[Schizosaccharomyces pombe] 75 58 231 229 1 29 847 gi|1205958 branchedchain aa transport system II carrier protein [Haemophilus 75 49 819influenzae] 230 2 518 1714 gi|971337 nitrite extrusion protein [Bacillussubtilis] 75 53 1197 231 1 1122 4 gi|1002521 MutL [Bacillus subtilis] 7554 1119 233 3 1314 1859 gi|467405 unknown [Bacillus subtilis] 75 59 546269 1 164 3 gi|1511246 methyl coenzyme M reductase system, component A2[Methanococcus jannaschii] 75 50 162 292 1 772 155 gi|1511604 M.jannaschii predicted coding region MJ1651 [Methanococcus jannaschii] 7546 618 304 4 1773 2261 gi|1205328 surfactin [Haemophilus influenzae] 7555 489 312 3 2437 3387 gi|285621 undefined open reading frame [Bacillusstearothermophilus] 75 62 951 312 5 4622 6403 gi|1041097 Pyruvate Kinase[Bacillus psychrophilus] 75 57 1782 319 1 353 877 gi|1212728 YqhI[Bacillus subtilis] 75 54 525 320 5 4321 5031 gi|1070361 OMPdecarboxylase [Lactococcus lactis] 75 56 711 320 6 5010 5642 gi|143394OMP-PRPP transferase [Bacillus subtilis] 75 60 633 337 4 1519 2088gi|487433 citrate synthase II [Bacillus subtilis] 75 58 570 394 2 6691271 gi|304976 matches PS00017: ATP_GTP_A and PS00301: EFACTOR_GTP;similar to longation 75 51 603 factor G, TetM/TetOtetracycline-resistance proteins Escherichia coli] 423 1 127 570gi|1183839 unknown [Pseudomonas aeruginosa] 75 59 444 433 2 1603 1929gi|149211 acetolactate synthase [Klebsiella pneumoniae] 75 63 327 446 2176 1540 gi|312441 dihydroorotase [Bacillus caldolyticus] 75 62 1365 4861 249 4 gi|1149682 potF gene product [Clostridium perfringens] 75 55 246496 1 3 794 gi|143582 spoIIIEA protein [Bacillus subtilis] 75 59 792 4982 824 1504 gi|143328 phoP protein (put.); putative [Bacillus subtilis]75 47 681 499 2 1061 1624 gi|1387979 44% identity over 302 residues withhypothetical protein from Synechocystis 75 51 564 sp, accessionD64006_CD; expression induced by environmental stress; some similarityto glycosyl transferases; two potential membrane-spanning helices[Bacillus subtil 568 1 453 265 pir|JC4110|JC41 triacylglycerol lipase(EC 3.1.1.3) 2 - Mycoplasma mycoides subsp. mycoides 75 50 189 (SGC3)613 2 233 36 gi|330993 tegument protein [Saimiriine herpesvirus 2] 75 75198 621 1 1 525 gi|529754 speC [Streptococcus pyogenes] 75 43 525 642 51809 2474 gi|1176401 EpiG [Staphylococcus epidermidis] 75 51 666 646 2454 657 gi|172442 ribonuclease P [Saccharomyces cerevisiae] 75 37 204657 1 3 347 gi|882541 ORF_o236 [Escherichia coli] 75 47 345 750 1 832 2gi|46971 epiP gene product [Staphylococcus epidermidis] 75 57 831 754 12 481 gi|1303901 YqhT [Bacillus subtilis] 75 57 480 763 2 393 223gi|1205145 multidrug resistance protein [Haemophilus influenzae] 75 51171 775 1 482 3 pir|B36889|B368 leuA protein, inactive - Lactococcuslactis subsp. lactis (strain IL1403) 75 63 480 793 1 1 180 gi|143316[gap] gene products [Bacillus megaterium] 75 57 180 800 1 160 2gi|509411 NFRA protein [Azorhizobium caulinodans] 75 34 159 811 1 560 3gi|143434 Rho Factor [Bacillus subtilis] 75 60 558 940 1 329 165gi|1276985 arginase [Bacillus caldovelox] 75 50 165 971 2 37 252gi|1001373 hypothetical protein [Synechocystis sp.] 75 58 216 1059 1 23280 gi|726480 L-glutamine-D-fructose-6-phosphate amidotransferase[Bacillus subtilis] 75 67 153 1109 2 219 374 gi|143331 alkalinephosphatase regulatory protein [Bacillus subtilis] 75 53 156pir|A27650|A27650 regulatory protein phoR - Bacillus subtilissp|P23545|PHOR_BACSU ALKALINE PHOSPHATASE SYNTHESIS SENSOR PROTEIN HOR(EC 2.7.3.—). 1268 1 137 3 gi|304135 ornithine acetyltransferase[Bacillus stearothermophilus] 75 63 135 sp|Q07908|ARGJ_BACST GLUTAMATEN-ACETYLTRANSFERASE (EC 2.3.1.35) ORNITHINE ACETYLTRANSFERASE)(ORNITHINE TRANSACETYLASE) (OATASE)/MINO-ACID ACETYLTRANSFERASE (EC2.3.1.1) (N-ACETYLGLUTAMATE YNTHA 1500 1 163 2 gi|1205488 excinucleaseABC subunit B [Haemophilus influenzae] 75 57 162 1529 1 400 2 gi|1002521MutL [Bacillus subtilis] 75 54 399 3010 1 387 4 gi|1204435 pyruvateformate-lyase activating enzyme [Haemophilus influenzae] 75 54 384 31051 1 180 gi|1041097 Pyruvate Kinase [Bacillus psychrophilus] 75 57 1803117 1 45 212 gi|899317 peptide synthetase module [Microcystisaeruginosa]pir|S49111|S49111 75 42 168 probable amino acid activatingdomain - Microcystis aeruginosa (fragment) (SUB 144-528) 3139 2 139 345gi|145294 adenine phosphoribosyl-transferase [Escherichia coli] 75 66207 3880 1 310 2 gi|1009366 Respiratory nitrate reductase [Bacillussubtilis] 75 58 309 3911 1 48 401 gi|433991 ATP synthase subunit beta[Bacillus subtilis] 75 68 354 3957 1 2 379 pir|D36889|D3683-isopropylmalate dehydratase (EC 4.2.1.33) chain leuC - Lactococcuslactis 75 65 378 subsp. lactis (strain IL1403) 4005 1 5 259 gi|216746D-lactate dehydrogenase [Lactobacillus plantarum] 75 48 255 4080 1 73333 gi|415855 deoxyribose aldolase [Mycoplasma hominis] 75 59 261 4111 11 339 gi|149435 putative [Lactococcus lactis] 75 57 339 4136 1 303 4gi|450688 hsdM gene of EcoprrI gene product [Escherichia coli]pir|S38437|S38437 hsdM 75 56 300 protein - Escherichia colipir|S09629|S09629 hypothetical protein A - Escherichia coli (SUB 40-520)4144 1 336 4 gi|48972 nitrate transporter [Synechococcus sp.] 75 49 3334237 1 374 84 gi|1339950 large subunit of NADH-dependent glutamatesynthase [Plectonema boryanum] 75 55 291 4306 2 73 318 gi|294260 majorsurface glycoprotein [Pneumocystis carinii] 75 68 246 4343 1 359 3gi|1204652 methylated-DNA-protein-cysteine methyltransferase[Haemophilus influenzae] 75 52 357 4552 1 312 4 gi|296464 ATPase[Lactococcus lactis] 75 55 309 38 9 5776 6126 gi|443793 NupC[Escherichia coli] 74 50 351 50 8 6221 5532 gi|1239988 hypotheticalprotein [Bacillus subtilis] 74 55 690 56 9 10770 12221 gi|1000451 TreP[Bacillus subtilis] 74 57 1452 64 2 1622 978 gi|41015 aspartate-tRNAligase [Escherichia coli] 74 57 645 66 6 4848 4633 gi|1212729 YqhJ[Bacillus subtilis] 74 47 216 67 18 14334 14897 gi|1510631 endoglucanase[Methanococcus jannaschii] 74 52 564 102 15 12561 13136 gi|149429putative [Lactococcus lactis] 74 67 576 102 16 13121 14419 gi|149435putative [Lactococcus lactis] 74 57 1299 108 4 3902 2931 gi|39478 ATPbinding protein of transport ATPases [Bacillus firmus] ir|S15486|S1548674 59 972 ATP-binding protein - Bacillus firmus p|P26946|YATR_BACFIHYPOTHETICAL ATP-BINDING TRANSPORT PROTEIN. 116 5 7093 5612 gi|1205430dipeptide transport system permease protein [Haemophilus influenzae 7449 1482 120 7 4342 4803 gi|146970 ribonucleoside triphosphate reductase[Escherichia coli] pir|A47331|A47331 74 58 462 anaerobic ribonucleotidereductase - Escherichia coli 121 7 5961 6581 gi|1107528 ttg start[Campylobacter coli] 74 51 621 128 3 2320 3531 gi|143318phosphoglycerate kinase [Bacillus megaterium] 74 57 1212 130 7 5237 5791gi|1256653 DNA-binding protein [Bacillus subtilis] 74 60 555 136 3 51503555 gi|143076 histidase [Bacillus subtilis] 74 58 1596 145 2 664 1368gi|407773 devA gene product [Anabaena sp.] 74 45 705 152 1 277 2gi|1377833 unknown [Bacillus subtilis] 74 54 276 164 10 11064 11375gi|580900 ORF3 gene product [Bacillus subtilis] 74 52 312 175 2 26242139 gi|642656 unknown [Rhizobium meliloti] 74 34 486 175 9 5612 5160gi|854656 Na/H antiporter system ORF2 [Bacillus alcalophilus] 74 46 453195 11 10339 9332 gi|1204430 hypothetical protein (SP: P25745)[Haemophilus influenzae] 74 55 1008 205 17 9059 8499 gi|1044979ribosomal protein L6 [Bacillus subtilis] 74 64 561 236 7 5574 6710gi|1146207 putative [Bacillus subtilis] 74 63 1137 241 3 3334 2147gi|694121 malate thiokinase [Methylobacterium extorquens] 74 52 1188 2466 2799 2293 gi|467374 single strand DNA binding protein [Bacillussubtilis] 74 64 507 249 4 5313 4075 gi|1524397 glycine betainetransporter OpuD [Bacillus subtilis] 74 55 1239 261 7 4081 3773gi|809542 CbrB protein [Erwinia chrysanthemi] 74 42 309 278 6 4665 3616gi|1204872 ATP-binding protein [Haemophilus influenzae] 74 54 1050 309 1666 112 gi|1205579 hypothetical protein (GB: U14003_302) [Haemophilusinfluenzae] 74 53 555 315 2 862 251 gi|143398 quinol oxidase [Bacillussubtilis] 74 57 612 320 1 1 1065 gi|143389 glutaminase of carbamylphosphate synthetase [Bacillus subtilis] 74 60 1065 pir|E39845|E39845carbamoyl-phosphate synthase glutamine-hydrolyzing) (EC 6.3.5.5),pyrimidine-repressible, small hain - Bacillus subtilis 380 2 382 1128gi|534857 ATPase subunit a [Bacillus stearothermophilus] 74 56 747 405 21311 880 gi|1303915 YqhZ [Bacillus subtilis] 74 65 432 433 5 2503 3270gi|473902 alpha-acetolactate synthase [Lactococcus lactis] 74 56 768 4521 1 942 gi|413982 ipa-58r gene product [Bacillus subtilis] 74 52 942 4611 3 1193 gi|558494 homoserine dehydrogenase [Bacillus subtilis] 74 511191 461 2 1174 1407 gi|40211 threonine synthase (thrC) (AA 1-352)[Bacillus subtilis] ir|A25364|A25364 74 56 234 threonine synthase (EC4.2.99.2) - Bacillus subtilis 462 2 402 734 gi|142520 thioredoxin[Bacillus subtilis] 74 62 333 478 1 320 66 gi|1499005 glycyl-tRNAsynthetase [Methanococcus jannaschii] 74 52 255 501 2 739 1740 gi|217040acid glycoprotein [Streptococcus pyogenes] 74 58 1002 551 2 2791 1499gi|143040 glutamate-1-semialdehyde 2,1-aminotransferase [Bacillussubtilis] 74 51 1293 pir|D42728|D42728 glutamate-1-semialdehyde2,1-aminomutase (EC .4.3.8) - Bacillus subtilis 573 1 1 477 gi|1006605hypothetical protein [Synechocystis sp.] 74 45 477 596 2 1298 816gi|1303853 YqgF [Bacillus subtilis] 74 55 483 618 2 1758 592 gi|114623721.4% of identity to trans-acting transcription factor of Sacharomyces74 55 1167 cerevisiae; 25% of identity to sucrose synthase of Zee mays;putative [Bacillus subtilis] 659 2 1269 1595 gi|1072380 ORF3[Lactococcus lactis] 74 62 327 724 1 188 3 gi|143374 phosphoribosylglycinamide synthetase (PUR-D; gtg start codon) Bacillus 74 58 186subtilis] 743 2 604 1209 gi|153833 ORF1; putative [Streptococcusparasanguis] 74 50 606 836 1 2 259 gi|143458 ORF V [Bacillus subtilis]74 47 258 989 2 443 724 gi|1303994 YqkM [Bacillus subtilis] 74 46 2821106 1 1 492 gi|46970 epiD gene product [Staphylococcus epidermidis] 7454 492 1135 2 373 528 gi|413948 ipa-24d gene product [Bacillus subtilis]74 48 156 1234 1 452 87 gi|495245 recJ gene product [Erwiniachrysanthemi] 74 36 366 2586 1 2 238 gi|1149701 sbcC gene product[Clostridium perfringens] 74 62 237 2959 1 400 2 gi|1405454 aconitase[Bacillus subtilis] 74 60 399 2962 1 363 76 gi|450686 3-phosphoglyceratekinase [Thermotoga maritima] 74 58 288 2983 1 3 191 gi|1303893 YqhL[Bacillus subtilis] 74 56 189 3018 1 2 223 gi|143040glutamate-1-semialdehyde 2,1-aminotransferase [Bacillus subtilis] 74 56222 pir|D42728|D42728 glutamate-1-semialdehyde 2,1-aminomutase (EC.4.3.8) - Bacillus' subtilis 3038 1 256 2 pir|S52915|S529 nitratereductase alpha chain - Bacillus subtilis (fragment) 74 57 255 3062 1189 4 gi|1107528 ttg start [Campylobacter coli] 74 51 186 4035 1 184 360gi|1022725 unknown [Staphylococcus haemolyticus] 74 64 177 4045 1 305 3gi|1510977 M. jannaachii predicted coding region MJ0938 [Methanococcusjannaschii] 74 41 303 4283 1 304 137 gi|520844 orf4 [Bacillus subtilis]74 58 168 4449 1 3 221 gi|580910 peptide-synthetase ORF1 [Bacillussubtilis] 74 54 219 4587 1 231 4 gi|1370207 orf6 [Lactobacillus sake] 7459 228 4603 1 29 214 gi|146208 glutamate synthase large subunit (EC2.6.1.53) [Escherichia coli] 74 60 186 pir|A29617|A29617 glutamatesynthase (NADPH) (EC 1.4.1.13) large hain- Escherichia coli 4670 1 184 2gi|1256135 YbbF [Bacillus subtilis] 74 61 183 5 10 7162 6371 gi|143727putative [Bacillus subtilis] 73 42 792 11 2 1372 290 gi|166338dihydroorotate dehydrogenase [Agrocybe aegerita] 73 55 1083 14 1 1020 16gi|143373 phosphoribosyl aminoimidazole carboxy formylormyltransferase/inosine 73 54 1005 monophosphate cyclohydrolase(PUR-H(J)) Bacillus subtilis] 23 5 4635 3844 gi|1468939meso-2,3-butanediol dehydrogenase (D-acetoin forming) [Klebsiella 73 58792 pneumoniae] 23 17 16360 15341 gi|297060 ornithine cyclodeaminase[Rhizobium meliloti] 73 37 1020 29 2 692 1273 gi|467442 stage Vsporulation [Bacillus subtilis] 73 54 582 31 5 4914 3361 gi|414000ipa-76d gene product [Bacillus subtilis] 73 55 1554 37 8 7402 6146gi|1429259 pepT gene product [Bacillus subtilis] 73 59 1257 37 9 75627386 gi|168367 alpha-isopropylmalate isomerase (put.); putative[Rhizomucor ircinelloides] 73 52 177 38 7 3931 4896 gi|405885 yeiN[Escherichia coli] 73 58 966 44 6 4238 3435 gi|580895 unknown [Bacillussubtilis] 73 53 804 44 11 7767 8306 gi|42009 moaB gene product[Eacherichia coli] 73 50 540 45 3 2439 3080 gi|1109685 ProW [Bacillussubtilis] 73 47 642 54 13 13794 13552 gi|413931 ipa-7d gene product[Bacillus subtilis] 73 61 243 59 4 1430 2248 gi|147923 threoninedehydratase 2 (EC 4.2.1.16) [Escherichia coli] 73 53 819 65 1 730 2gi|677944 AppF [Bacillus subtilis] 73 56 729 80 2 860 345 gi|580932 murDgene product [Bacillus subtilis] 73 53 516 102 13 10124 11179 gi|5808913-isopropylmalate dehydrogenase (AA 1-365) [Bacillus subtilis] 73 551056 pir|A26522|A26522 3-isopropylmalate dehydrogenase (EC 1.1.1.85) -Bacillus subtilis 109 2 2600 1707 gi|1510849 M. jannaschii predictedcoding region MJ0775 [Methanococcus jannaschii] 73 40 894 120 8 47825756 gi|146970 ribonucleoside triphosphate reductase [Escherichia coli]pir|A47331|A47331 73 56 975 anaerobic ribonucleotide reductase -Escherichia coli 120 9 5726 6223 gi|1204333 anaerobicribonucleoside-triphosphate reductase [Haemophilus influenzae] 73 62 498132 5 4151 4363 gi|871048 HPSR2 - heavy chain potential motor protein[Giardia inrestinalis] 73 43 213 140 6 4324 2696 gi|634107 kdpB[Eacherichia coli] 73 59 1629 142 6 5939 4918 gi|410125 ribG geneproduct [Bacillus subtilis] 73 57 1122 149 4 1717 1568 gi|460892 heparinbinding protein-44, HBP-44 [mice, Peptide, 360 aa] 73 53 150pir|JX0281|JX0281 heparin-binding protein-44 precursor - mouse gi|220434ORF [Mus musculus] (SUB 2-360) 158 1 1 1431 gi|882504 ORF_f560[Eacherichia coli] 73 57 1431 174 6 4525 3698 gi|1146240 ketopantoatehydroxymethyltransferase [Bacillus subtilis] 73 55 828 175 8 5178 4819gi|854657 Na/H antiporter system ORF3 [Bacillus alcalophilus) 73 56 360186 5 5493 4393 gi|467477 unknown [Bacillus subtilis] 73 48 1101 249 65729 5175 gi|1524397 glycine betaine transporter OpuD [Bacillussubtilis] 73 56 555 265 4 1873 2280 gi|39848 U3 [Bacillus subtilis] 7341 408 270 1 328 582 gi|780461 220 kDa polyprotein [African swine fevervirus] 73 53 255 278 4 3618 2953 gi|1208965 hypothetical 23.3 kd protein[Eacherichia coli] 73 49 666 279 3 3593 2202 gi|1185288 isochorismatesynthase [Bacillus subtilis] 73 58 1392 291 4 1207 1575 gi|1511440glutamine - fructose-6-phosphate transaminase (Methanococcus jannaschii)73 63 369 299 2 735 1166 gi|467437 unknown [Bacillus subtilis] 73 58 432299 5 2050 3234 gi|467439 temperature sensitive cell division [Bacillussubtilis] 73 53 1185 334 1 728 219 gi|536655 ORF YBR244w [Saccharomycescerevisise] 73 43 510 336 2 1036 245 gi|790943 urea amidolyase [Bacillussubtilis] 73 51 792 374 3 1389 1874 gi|1405451 YneJ [Bacillus subtilis]73 55 486 433 4 1916 2554 gi|473902 alpha-aceholactate synthase[Lactococcus lactis] 73 54 639 509 2 1028 261 gi|467483 unknown[Bacillus subtilis] 73 56 768 513 1 918 127 gi|1146220 NAD+ dependentglycerol-3-phosphate dehydrogenase [Bacillus subtilis] 73 56 792 533 2239 733 gi|1510605 hypothetical protein (SP: P42297) [Methanococcusjannaschii] 73 44 495 546 2 1148 2815 gi|41748 hsdM protein (AA 1-520)[Eacherichia coli] 73 52 1668 549 1 382 2 gi|1314847 CinA [Bacillussubtilis] 73 57 381 567 1 675 4 gi|410137 ORFX13 [Bacillus subtilis] 7358 672 716 2 654 1112 gi|1256623 exodeoxyribonuclease [Bacillussubtilis] 73 56 459 772 1 3 677 gi|142010 Shows 70.2% similarity and48.6% identity to the EnvM protein of almonella 73 57 675 typhimurium[Anabaena sp.] 774 1 3 209 gi|409286 bmrU [Bacillus subtilis] 73 52 207782 1 1 402 gi|143320 [gap] gene products [Bacillus megaterium] 73 56402 789 2 451 762 gi|1063246 low homology to P14 protein of Heamophilusinfluenzar and 14.2 kDa protein 73 56 312 of Escherichia coli [Bacillussubtilis] 796 1 3 911 gi|853754 ABC transporter [Bacillus subtilis] 7358 909 806 3 949 689 gi|143786 tryptophanyl-tRNA synthetase (EC 6.1.1.2)[Bacillus subtilis] 73 51 261 pir|JT0481|YWBS tryptophan-tRNA ligase (EC6.1.1.2) - Bacillus subtilis 816 2 3097 1355 gi|41748 hsdM protein (AA1-520) [Escherichia coli] 73 52 1743 839 1 400 2 gi|886906argininosuccinate synthetase [Streptomyces clavuligerus]pir|S57659|S57659 73 59 399 argininosuccinate synthase (EC 6.3.4.5) -treptomyces clavuligerus 857 1 3 290 gi|348052 acetoin utilizationprotein [Bacillus subtilis] 73 50 288 1008 1 398 6 gi|40100 rodC (tag3)polypeptide (AA 1-746) [Bacillus subtilis] ir|S06049|S06049 73 41 393rodC protein - Bacillus subtilis p|P13485|TAGF_BACSU TECHOIC ACIDBIOSYNTHESIS PROTEIN F. 1018 1 1 213 gi|529357 No definition line found[Caenorhabditis elegans] sp|P46975|STT3_CAEEL 73 53 213 OLIGOSACCHARYLTRANSFERASE STT3 SUBUNIT OMOLOG. 1033 1 3 491 gi|142706 comG1 geneproduct [Bacillus subtilis] 73 51 489 1174 1 204 13 gi|1149513 alpha3asubunit of laminin 5 [Homo sapiens] 73 60 192 1175 1 329 3 gi|473817‘ORF’ [Escherichia coli] 73 57 327 1187 1 3 209 gi|580870 ipa-37d qoxAgene product [Bacillus subtilis] 73 52 207 1206 1 72 245 gi|144816formyltetrahydrofolate synthetase (FTHFS) (ttg start codon) (EC .3.4.3)73 43 174 [Moorella thermoacetica] 1454 1 241 59 gi|1213253 unknown[Schizosaccharomyces pombe] 73 53 183 1469 1 260 3 gi|1303787 YqeG[Bacillus subtilis] 73 55 258 1761 1 189 4 gi|9135 Mst26Aa gene product[Drosophila simulans] 73 34 186 1849 1 243 19 gi|162307 DNAtopoisomerase II [Trypanosoma cruzi] 73 60 225 2055 1 2 400 gi|559381P47K protein [Rhodococcus erythropolis] 73 34 399 2556 1 2 244 gi|145925fecB [Escherichia coli] 73 62 243 2947 2 400 251 gi|1184680polynucleotide phosphorylase [Bacillus subtilis] 73 51 150 2956 1 375 4gi|143397 quinol oxidase [Bacillus subtilis] 73 58 372 3037 1 329 3gi|143091 acetolactate synthase [Bacillus subtilis] 73 55 327 3115 1 1943 gi|323866 overlapping out-of-phase protein [Eggplant mosaic virus] 7353 192 sp|P20129|V70K_EPMV 70 KD PROTEIN. 3603 2 527 354 gi|1439521glutaryl-CoA dehydrogenase precursor [Mus musculus] 73 48 174 3743 1 4002 gi|450688 hsdM gene of EcoprrI gene product [Escherichiacoli]pir|S38437|S38437 hsdM 73 54 399 protein - Escherichia colipir|S09629|S09629 hypothetical protein A - Escherichia coli (SUB 40-520)3752 1 359 78 gi|1524193 unknown (Mycobacterium tuberculosis] 73 59 2823852 1 2 181 gi|216746 D-lactate dehydrogenase [Lactobacillus plantarum]73 68 180 3914 1 239 3 pir|S13490|S134 Hydroxymethylglutaryl-CoAsynthase (EC 4.1.3.5) - Chicken (fragment) 73 53 237 3914 2 343 116gi|528991 unknown [Bacillus subtilis] 73 38 228 4069 1 2 316 gi|40003oxoglutarate dehydrogenase (NADP+) [Bacillus subtilis]p|P23129|OD01_BACSU 73 55 315 2-OXOGLUTARATE DEHYDROGENASE E1 COMPONENT(EC 2.4.2) (ALPHA-KETOGLUTARATE DEHYDROGENASE). 4165 1 365 15 gi|1439521glutaryl-CoA dehydrogenase precursor [Mus musculus] 73 48 351 4196 1 1177 gi|809660 deoxyribose-phosphate aldolase [Bacillus subtilis]pir|S49455|S49455 73 60 177 deoxyribose-phosphate aldolase (EC4.1.2.4) - Bacillus subtilis 4202 1 378 184 gi|528991 unknown [Bacillussubtilis) 73 38 195 4314 1 2 193 gi|436797 N-acyl-L-amino acidamidohydrolase [Bacillus stearothermophilus] 73 47 192sp|P37112|AMA_BACST N-ACYL-L-AMINO ACID AMIDOHYDROLASE (EC .5.1.14)(AMINOACYLASE). 4393 1 3 263 gi|216267 ORF2 [Bacillus megaterium) 73 47261 35 2 903 1973 gi|1146196 phosphoglycerate dehydrogenase [Bacillussubtilis] 72 53 1071 38 22 17877 16660 gi|602031 similar totrimethylamine DH [Mycoplasma capricolum] pir|S49950|S49950 72 54 1218probable trimethylamine dehydrogenase (EC .5.99.7) - Mycoplasmacapricolum (SGC3) (fragment) 38 23 18134 19162 gi|413968 ipa-44d geneproduct [Bacillus subtilis] 72 54 1029 44 19 11895 12953 gi|516272unknown [Bacillus subtilis] 72 49 1059 48 7 6248 7117 gi|43499 pyruvatesynthase [Halobacterium halobium) 72 49 870 50 7 5691 4819 gi|1205399proton glutamate symport protein [Haemophilus influenzae] 72 53 873 53 99259 7997 gi|1303956 YqjE [Bacillus subtilis] 72 52 1263 56 23 2954929995 gi|467471 unknown [Bacillus subtilis] 72 47 447 69 4 4123 2948gi|1354775 pfoS/R [Treponema pallidum] 72 46 1176 69 5 4377 4982gi|904198 hypothetical protein [Bacillus subtilis] 72 43 606 73 1 2 856gi|142997 glycerol uptake facilitator [Bacillus subtilis] 72 59 855 9813 9371 10258 gi|467435 unknown [Bacillus subtilis] 72 50 888 127 1 11593 gi|217144 alanine carrier protein [thermophilic bacterium PS3]pir|A45111|A45111 72 56 1593 alanine transport protein - thermophilicacterium PS-3 131 1 2600 3 gi|153952 polymerase III polymerase subunit(dnaE) [Salmonella typhimurium] 72 53 2598 pir|A45915|A45915DNA-directed DNA polymerase (EC 2.7.7.7) III lpha chain - Salmonellatyphimurium 141 4 1040 1978 gi|1405446 transketolase [Bacillus subtilis]72 54 939 149 8 2535 2251 gi|606234 secY [Escherichia coli] 72 44 285149 17 5245 5018 gi|1304472 DNA polymerase [Unidentified phycodnavirusclone OTU4] 72 55 228 154 1 1 210 gi|1205620 ferritin like protein[Haemophilus influenzae] 72 40 210 155 1 1320 433 gi|391610 farnesyldiphosphate synthase [Bacillus stearothermophilus] 72 57 888pir|JX0257|JX0257 geranyltranstransferase (EC 2.5.1.10) - Bacillusstearothermophilus 180 1 2 328 gi|433630 A180 [Saccharomyces cerevisiae]72 62 327 184 3 1145 3553 gi|1205110 virulence associated proteinhomolog [Haemophilus influenzae] 72 49 2409 195 2 1279 635 gi|1001730hypothetical protein [Synechocystis sp.] 72 45 645 206 13 14646 15869gi|1064807 ORTHININE AMINOTRANSFERASE [Bacillus subtilis] 72 50 1224 2092 462 932 gi|1204666 hypothetical protein (GB: X73124_53) [Haemophilusinfluenzae] 72 60 471 215 2 522 280 gi|881513 insulin receptor homolog[Drosophila melanogaster] pir|S57245|S57245 72 63 243 insulin receptorhomolog - fruit fly (Drosophila elanogaster) (SUB 46- 2146) 224 1 2 790gi|949974 sucrose repressor [Staphylococcus xylosus] 72 54 789 233 1 7654 gi|1408493 homologous to SwissProt: YIDA_ECOLI hypothetical protein[Bacillus subtilis] 72 52 762 240 1 220 1485 gi|537049 ORF_o470[Escherichia coli] 72 52 1266 245 1 3 1340 gi|1204578 hypotheticalprotein (GB: U06949_1) [Haemophilus influenzae] 72 46 1338 259 2 1245382 gi|1340128 ORF1 [Staphylococcus aureus] 72 59 864 304 2 285 1094gi|1205330 glutamine-binding periplasmic protein [Haemophilusinfluenzae] 72 52 810 307 10 5039 4752 gi|1070015 protein-dependent[Bacillus subtilis] 72 53 288 315 1 260 3 gi|143399 quinol oxidase[Bacillus subtilis] 72 55 258 316 11 9308 8994 gi|1204445 hypotheticalprotein (SP: P27857) [Haemophilus influenzae] 72 52 315 337 3 926 1609gi|487433 citrate synthase II [Bacillus subtilis] 72 55 684 364 7 104938448 gi|1510643 ferrous iron transport protein B [Methanococcusjannaschii] 72 53 2046 409 2 340 1263 gi|1402944 orfRM1 gene product[Bacillus subtilis] 72 49 924 441 3 1590 1003 gi|312379 highly conservedamong eubacteria [Clostridium acetobutylicum] 72 48 588pir|S34312|S34312 hypothetical protein V - Clostridium cetobutylicum 4536 2505 2356 pir|S00601|BXSA antibacterial protein 3 - Staphylococcushaemolyticus 72 70 150 460 1 2 625 gi|1016162 ABC transporter subunit[Cyanophora paradoxa] 72 51 624 463 1 1628 3 gi|666014 The polymorphysm(RFLP) of this gene is associated with usceptibility to 72 60 1626essential hypertension. The SA gene product has light homology toacetyl- CoA synthetase [Homo sapiens] 480 4 3047 3466 gi|433992 ATPsynthase subunit epsilon [Bacillus subtilis] 72 53 420 502 1 586 86gi|310859 ORF2 [synechococcus sp.] 72 50 501 519 1 81 1184 gi|1303704YrkE [Bacillus subtilis] 72 54 1104 559 1 3 746 gi|1107530 ceuD geneproduct [Campylobacter coli] 72 56 744 575 1 573 4 gi|1303866 Yqgs[Bacillus subtilis] 72 56 570 671 1 2 592 gi|1204497 protein-exportmembrane protein [Haemophilus influenzae] 72 44 591 679 2 295 1251gi|563258 virulence-associated protein E [Dichelobacter nodosus] 72 52957 687 2 295 957 gi|1146214 44% identical amino acids with theEscherichia coli smba supress; putative 72 49 663 [Bacillus subtilis]837 1 1 435 gi|1146183 putative [Bacillus subtilis] 72 54 435 868 1 150788 gi|1377842 unknown [Bacillus subtilis] 72 55 639 922 1 130 432gi|1088269 unknown protein [Azotobacter vinelandii] 72 58 303 941 1 2238 gi|153929 NADPH-sulfite reducatase flavoprotein component[Salmonella yphimurium] 72 49 237 980 1 421 2 gi|853767UDP-N-acetylglucosamine 1-carboxyvinyltransferase [Bacillus subtilis] 7259 420 1209 1 213 43 gi|144735 neurotoxin type B [Clostridium botulinum]72 44 171 1469 2 474 277 gi|1205458 hypothetical protein (GB: D26562_47)[Haemophilus influenzae] 72 63 198 1956 1 365 3 gi|154409hexosephosphate transport protein [Salmonella typhimurium] 72 44 363pir|B41853|B41853 hexose phosphate transport system regulatory roteinuhpB - salmonella typhimurium 2101 1 3 401 gi|1303950 YqiY [Bacillussubtilis] 72 50 399 2503 1 399 229 gi|149713 formate dehydrogenase[Methanobacterium formicicum] pir|A42712|A42712 72 56 171 formatedehydrogenase (EC 1.2.1.2) - Methanobacterium formicicum 2967 1 3 155gi|1212729 YqhJ [Bacillus subtilis] 72 46 153 3004 1 185 3 gi|665999hypothetical protein [Bacillus subtilis] 72 55 183 3109 1 141 4gi|413968 ipa-44d gene product [Bacillus subtilis] 72 45 138 3171 1 3287 gi|515938 glutamate synthase (ferredoxin) [Synechocystis sp.]pir|S46957|S46957 72 52 285 glutamate synthase (ferredoxin) (EC1.4.7.1) - Synechocystis sp. 3771 1 26 367 gi|1408501 homologous toN-acyl-L-amino acid amidohydrolase of Bacillus 72 63 342stearothermophilus [Bacillus subtilis] 3951 1 1 222 gi|1500409 M.jannaschii predicted coding region MJ1519 [Methanococcus jannaschii] 7238 222 4190 1 362 3 gi|39956 IIGlc [Bacillus subtilis] 72 57 360 4444 13 347 gi|1009366 Respiratory nitrate reductase [Bacillus subtilis] 72 55345 6 2 931 1200 gi|537095 ornithine carbamoyltransferase [Escherichiacoli] 71 55 270 11 15 10859 10368 gi|532309 25 kDa protein [Escherichiacoli] 71 47 492 19 2 1248 2435 gi|1244574 D-alanine; D-alanine ligase[Enterococcus hirae] 71 52 1188 21 2 898 1488 gi|149629 anthranilatesynthase component 2 [Leptospira biflexa] pir|C32840|C32840 71 45 591anthranilate synthase (EC 4.1.3.27) component II Leptospira biflexa 34 11 567 gi|1303983 YqkF [Bacillus subtilis] 71 59 567 37 3 2806 2420gi|1209681 glutamate-rich protein [Bacillus firmus] 71 50 387 38 1812250 12462 gi|927645 arginyl endopeptidase [Porphyromonas gingivalis]71 50 213 39 3 1246 4431 pir|S09411|S094 spoIIIE protein - Bacillussubtilis 71 49 3186 53 14 14760 13750 gi|142611 branched chainalpha-keto acid dehydrogenase E1-alpha [Bacillus subtilis] 71 58 1011 5411 12625 11789 gi|143014 gnt repressor [Bacillus subtilis] 71 46 837 577 5860 4568 gi|508175 EIIC domain of PTS-dependent Gat transport andphosphorylation Escherichia 71 48 1293 coli] 57 18 13897 14334gi|1063247 high homology to flavohemoprotein (Haemoglobin-like protein)of Alcaligenes 71 56 438 eutrophus and Saccharomyces cerevisiae[Bacillus subtilis] 62 16 9831 10955 gi|1303926 YgiG [Bacillus subtilis]71 54 1125 70 12 8505 8966 gi|147198 phnE protein [Escherichia coli] 7138 462 86 5 2089 1784 gi|904205 hypothetical protein [Bacillus subtilis]71 51 306 96 7 7601 8269 gi|709991 hypothetical protein [Bacillussubtilis] 71 49 669 100 6 4822 5931 gi|1060848 Opine dehydrogenase[Arthrobacter sp.] 71 45 1110 103 1 532 2 gi|143089 iep protein[Bacillus subtilis] 71 41 531 109 18 15312 15695 gi|413985 ipa-61d geneproduct [Bacillus subtilis] 71 57 384 113 1 316 2 gi|663254 probableprotein kinase [Saccharomyces cerevisiae] 71 57 315 114 5 5603 4608gi|143156 membrane bound protein [Bacillus subtilis] 71 40 996 133 21723 359 gi|1303913 YqhX [Bacillus subtilis] 71 53 1365 149 19 5895 5455gi|529650 G40P [Bacteriophage SPP1] 71 51 441 154 5 3087 2539 gi|425488repressor protein [Streptococcus sobrinus] 71 47 549 164 11 11354 11689gi|49318 ORF4 gene product [Bacillus subtilis] 71 52 336 169 5 1936 2745gi|1403403 unknown [Mycobacterium tuberculosis] 71 56 810 193 2 272 1234gi|1303788 YqeH [Bacillus subtilis] 71 49 963 205 1 895 47 gi|1215694GlnQ [Mycoplasma pneumoniae] 71 46 849 233 4 1849 2022 gi|633732 ORF1[Campylobacter jejuni] 71 50 174 237 7 4501 5169 gi|149384 HisIE[Lactococcus lactis] 71 54 669 272 4 2273 1698 gi|709993 hypotheticalprotein [Bacillus subtilis] 71 48 576 274 2 618 1496 gi|143035 NAD(P)H:glutamyl-transfer RNA reductase [Bacillus subtilis] 71 53 879pir|A35252|A35252 5-aminolevulinate synthase (EC 2.3.1.37) - Bacillussubtilis 276 5 2720 2091 gi|303562 ORF210 [Escherichia coli] 71 50 630287 1 136 660 gi|310634 20 kDa protein [Streptococcus gordonii] 71 53525 288 6 2771 2220 gi|1256625 putative [Bacillus subtilis] 71 47 552301 6 2461 1430 gi|467417 similar to lysine decarboxylase [Bacillussubtilis] 71 57 1032 306 4 5222 3837 gi|1256618 transport protein[Bacillus subtilis] 71 56 1386 307 2 925 314 gi|602683 orfC [Mycoplasmacapricolum] 71 45 612 310 5 5146 4499 gi|348052 acetoin utilizationprotein [Bacillus subtilis] 71 51 648 322 1 2 1303 gi|1001819hypothetical protein [Synechocystis sp.] 71 46 1302 333 4 3995 3819gi|467473 unknown [Bacillus subtilis] 71 57 177 350 2 548 922 gi|551879ORF 1 [Lactococcus lactis] 71 55 375 375 4 1860 3071 gi|467447 unknown[Bacillus subtilis] 71 57 1212 380 5 1560 2102 gi|142557 ATP synthase bsubunit [Bacillus megaterium] 71 43 543 414 2 251 637 gi|580904homologous to E. coli rnpA [Bacillus subtilis] 71 49 387 424 1 335 1354gi|581305 L-lactate dehydrogenase [Lactobacillus plantarum] 71 57 1020436 4 3270 2839 pir|PN0501|PN05 phosphoribosylanthranilate isomerase (EC5.3.1.24) - Bacillus subtilis 71 66 432 [fragment] 482 1 3 1280gi|410142 ORFX18 [Bacillus subtilis] 71 49 1278 525 3 1844 1416gi|143370 Phosphoribosylpyrophosphate amidotransferase [PUR-F; EC2.4.2.14] Bacillus 71 56 429 subtilis] 529 4 2047 1355 gi|606150ORF_f309 [Escherichia coli] 71 43 693 563 1 22 969 gi|1237015 ORF4[Bacillus subtilis] 71 53 948 581 1 255 4 gi|1301730 T25G3.2[Caenorhabditis elegans] 71 47 252 612 2 913 758 gi|153968 fimbriae Z[Salmonella typhimurium] 71 55 156 613 1 1 654 gi|466778 lysine specificpermease [Escherichia coli] 71 50 654 618 1 623 3 gi|1146238 poly(A)polymerase [Bacillus subtilis] 71 52 621 630 1 586 2 gi|1486243 unknown[Bacillus subtilis] 71 53 585 691 1 641 156 gi|289260 comE ORF1[Bacillus subtilis] 71 51 486 694 2 149 427 gi|12971 NADH dehydrogenasesubunit V (AA 1-605) [Gallus gallus] ir|s10197|S10197 71 47 279 NADHdehydrogenase (ubiquinone) (EC 1.6.5.3) chain - chicken mitochondrion(SGC1) 715 2 169 777 gi|1303830 YqfL [Bacillus subtilis] 71 53 609 746 2970 467 gi|1377843 unknown [Bacillus subtilis] 71 52 504 748 1 802 167gi|1405459 YneS [Bacillus subtilis] 71 49 636 753 1 524 30 gi|1510389 M.jannaschii predicted coding region MJ0296 [Methanococcus jannaschii] 7153 495 761 1 3 215 gi|475972 pentafunctional enzyme [Pneumocystiscarinii] 71 47 213 783 1 703 203 gi|536655 ORF YBR244w [Saccharomycescerevisiae] 71 52 501 800 3 987 682 gi|1204326 tRNA delta(2)-isopentenylpyrophosphate transferase [Haemophilus influenzae] 71 48306 806 1 116 286 gi|1419075 cbiM gene product [Methanobacteriumthermoautotrophicum] 71 50 171 931 1 488 3 gi|893358 PgsA [Bacillussubtilis] 71 56 486 1041 1 2 262 gi|1408507 pyrimidine nucleosidetransport protein [Bacillus subtilis] 71 45 261 1070 1 2 172 gi|709993hypothetical protein [Bacillus subtilis] 71 46 171 1176 1 57 365gi|151259 HMG-CoA reductase (EC 1.1.1.88) [Pseudomonas mevalonii]pir|A44756|A44756 71 49 309 hydroxymethylglutaryl-CoA reductase (EC1.1.1.88) Pseudomonas sp. 1181 1 184 2 gi|46971 epiP gene product[Staphylococcus epidermidis] 71 50 183 1281 1 3 290 gi|153016 ORF 419protein [Staphylococcus aureus] 71 50 288 1348 1 229 2 gi|602683 orfc[Mycoplasma capricolum] 71 48 228 2002 1 379 2 gi|1008177 ORF YJL046w[Saccharomyces cerevisiae] 71 48 378 2119 1 2 217 gi|1046088arginyl-tRNA synthetase [Mycoplasma genitalium] 71 50 216 2418 1 3 320gi|1499771 M. jannaschii predicted coding region MJ0936 [Methanococcusjannaschii] 71 57 318 2961 1 2 187 gi|312443 carbamoyl-phosphatesynthase (glutamine-hydrolysing) [Bacillus aldolyticus] 71 57 186 2999 267 306 gi|710020 nitrite reductase (nirB) [Bacillus subtilis] 71 43 2403033 1 2 184 gi|1262335 YmaA [Bacillus subtilis] 71 57 183 3584 1 3 338gi|401716 beta-isopropylmalate dehydrogenase [Neurospora crassa] 71 55336 3715 2 399 55 gi|563952 gluconate permease [Bacillus licheniformis]71 59 345 3785 1 387 4 gi|47382 acyl-CoA-dehydrogenase [Streptomycespurpurascens] 71 57 384 3875 1 272 3 gi|1001541 hypothetical protein[Synechocystis sp.] 71 38 270 4135 1 320 3 gi|142695S-adenosyl-L-methionine: uroporphyrinogen III methyltransferase Bacillus71 52 318 megaterium] 4249 1 63 239 gi|1205363 deoxyribose aldolase[Haemophilus influenzae] 71 63 177 4508 1 267 4 gi|1197667 vitellogenin[Anolis pulchellus] 71 46 264 1976 1 237 22 gi|9806 lysine-rich asparticacid-rich protein [Plasmodium chabaudi] 56 33 216 r|S22183|S22183lysine/aspartic acid-rich protein - Plasmodiom baudi 2161 1 2 400gi|1237015 ORF4 [Bacillus subtilis] 56 27 399 2958 1 183 4 gi|466685 Nodefinition line found [Escherichia coli] 56 26 180 2979 1 212 3gi|1204354 spore germination and vegetative growth protein [Haemophilusinfiuenzae] 56 40 210 2994 2 326 126 gi|836646phosphoribosylformimino-praic ketoisomerase [Rhodobacter phaeroides] 5629 201 3026 1 179 328 gi|143306 penicllin V amidase [Bacillussphaericus] 56 30 150 3189 1 146 3 gi|1166604 Similar to aldehydedehydrogenase [Caenorhabditis elegans] 56 37 144 3770 1 63 401gi|1129145 acetyl-CoA C-acyltransferase [Mangifera indica] 56 43 3394054 2 361 2 gi|1205355 Na+/H+ antiporter [Haemophilus influenzae] 56 31360 4145 1 1 324 gi|726095 long-chain acyl-CoA dehydrogenase [Musmusculus] 56 36 324 4200 1 254 3 gi|155588 glucose-fructoseoxidoreductase [Zymomonas mobilis|pir|A42289|A42289 56 40 252glucose-fructose oxidoreductase (EC 1.1.—.—) recursor - Zymomonasmobilis 4273 1 355 35 gi|308861 GTG start codon [Lactococcus lactis] 5633 321 1 3 3436 2777 gi|5341 Putative orF YCLX8c, len: 192[Saccharomyces cerevisiae] r|S53591|S53591 55 25 660 hypotheticalprotein - yeast (Saccharomyces evisiae) 11 12 8505 7633 gi|216773haloacetate dehalogenase H-1 [Moraxella sp.] 55 32 873 12 4 4534 3935gi|467337 unknown [Bacillus subtilis] 55 26 600 19 5 5404 5844gi|1001719 hypothetical protein [Synechocystis sp.] 55 25 441 23 1312339 10591 gi|474190 iucA gene product [Escherichia coli] 55 30 1749 327 5368 6888 gi|1340096 unknown [Mycobacterium tuberculosis] 55 37 152134 3 1808 1047 gi|1303968 YqjQ [Bacillus subtilis] 55 39 762 34 5 34122864 gi|1303962 Yqjk [Bacillus subtilis] 55 33 549 36 1 647 3 gi|606045ORF_o118 [Escherichia coli] 55 27 645 36 6 5243 4266 gi|1001341hypothetical protein [Synechocystis sp.] 55 31 978 47 3 3054 3821gi|1001819 hypothetical protein [Synechocystis sp.] 55 21 768 49 1 1127189 gi|403373 glycerophosphoryl diester phosphodiesterase [Bacillussubtilis] 55 36 939 pir|S37251|S37251 glycerophosphoryl diesterphosphodiesterase - Bacillus subtilis 67 11 8966 9565 gi|153053 norA1199protein [Staphylococcus aureus] 55 23 600 75 3 881 1273 gi|41698L-histidinol: NAD+ oxidoreductase (EC 1.1.1.23) (aa 1-434) Escherichiacoli) 55 33 393 82 9 14194 13001 gi|1136221 carboxypeptidase [Sulfolobussolfataricus] 55 35 1194 87 4 3517 4917 gi|1064812 function unknown[Bacillus subtilis] 55 26 1401 88 2 1172 1636 gi|882463protein-N(pi)-phosphohistldine-sugar phosphotransferase [Escherichiacoli] 55 35 465 92 1 127 516 gi|1377832 unknown [Bacillus subtilis] 5536 390 100 2 836 2035 gi|1370274 zeaxanthin epoxidase [Nicotianaplumbaginifolia] 55 36 1200 100 5 4658 4179 gi|396660 unknown openreading frame [Buchnera aphidicola] 55 29 480 108 3 2986 1706 gi|1499866M. jannaschii predicted coding region MJ1024 [Methanococcus jannaschli]55 31 1281 114 3 1834 1052 gi|1511367 formate dehydrogenase, alphasubunit [Methanococcus jannaschii] 55 29 783 144 3 1476 1147 gi|1100787unkown [Saccharomyces cerevisiae] 55 35 330 165 5 5508 4804 gi|1045884M. genitalium predicted coding region MG199 [Hycoplasma genitalium] 5527 705 189 5 2205 2576 gi|142569 ATP synthase a subunit [Bacillusfirmus] 55 35 372 191 6 6857 4578 gi|559411 B0272.3 [Caenorhabditiselegans] 55 39 2280 194 2 364 636 gi|1145768 K7 kinesin-like protein[Dictyostelium discoideum] 55 34 273 209 4 1335 1676 gi|473357 thi4 geneproduct [Schizosaccharomyces pombe] 55 35 342 211 2 1145 597 gi|410130ORFX6 [Bacillus subtilis] 55 37 549 213 2 644 1372 gi|633692 TrsA[Yersinia enterocolitica] 55 28 729 214 7 4144 5481 gi|1001793hypothetical protein [Synechocystis sp.] 55 30 1338 221 7 9197 6921gi|466520 pocR [Salmonella typhimurium] 55 32 2277 233 8 4817 3726gi|1237063 unknown [Mycobacterium tuberculosis] 55 38 1092 236 4 13752340 gi|1146199 putative [Bacillus subtilis] 55 32 966 243 2 380 1885gi|459907 mercuric reductase (Plasmid pI258] 55 29 1506 258 1 394 2gi|455006 orf6 [Rhodococcus fascians] 55 36 393 281 1 126 938 gi|1408493homologous to SwissProt: YIDA_ECOLI hypothetical protein [Bacillussubtilis] 55 35 813 316 3 1323 2102 gi|1486447 LuxA homologue [Rhizobiumsp.] 55 30 780 326 5 2744 2520 gi|1296824 proline iminopeptidase[Lactobacillus helveticus] 55 36 225 351 2 1429 536 gi|1204820 hydrogenperoxide-inducible activator [Haemophilus influenzae] 55 28 894 353 42197 2412 gi|1272475 chitin synthase [Emericella nidulans] 55 50 216 3801 14 379 gi|142554 ATP synthase i subunit [Bacillus megaterium] 55 37366 383 1 232 2 gi|289272 ferrichrome-binding protein [Bacillussubtilis] 55 36 231 386 1 3 938 gi|1510251 DNA helicase, putative[Methanococcus jannaschii] 55 30 936 410 2 1208 1891 gi|1205144multidrug resistance protein [Haemophilus influenzae] 55 27 684 483 2411 833 gi|413934 ipa-10r gene product [Bacillus subtilis] 55 26 423 5293 1433 1089 gi|606150 ORF_f309 [Escherichia coli] 55 33 345 555 1 585 82gi|143407 para-aminobenzoic acid synthase, component I (pab) [Bacillussubtilis] 55 28 504 565 1 202 2 gi|1223961 CDP-tyvelose epimerase[Yersinia pseudotuberculosis] 55 41 201 582 1 452 153 gi|1256643 20.2%identity with NADH dehydrogenase of the Leishmania major 55 36 300mitochondrion; putative [Bacillus subtilis] 645 5 2057 1854 gi|210824fusion protein F [Bovine respiratory syncytial virus] pir|JQ1481|VGNZBA55 25 204 fusion glycoprotein precursor - bovine espiratory syncytialvirus (strain A51908) 672 2 957 2216 gi|1511333 M. jannaschii predictedcoding region MJ1322 [Methanococcus jannaschii] 55 36 1260 730 1 479 3gi|537007 ORF_f379 [Escherichia coli] 55 30 477 737 1 945 31 gi|536963CG Site No. 18166 [Escherichia coli] 55 30 915 742 2 228 572 gi|304160product unknown [Bacillus subtilis] 55 38 345 817 2 903 595 gi|1136289histidine kinase A [Dictyostelium discoideum] 55 29 309 819 1 355 128gi|558073 polymorphic antigen [Plasmodium falciparum] 55 22 228 832 2724 296 gi|40367 ORFC [Clostridium acetobutylicum] 55 32 429 840 1 386 3gi|1205875 pseudouridylate synthase I [Haemophilus influenzae] 55 39 3841021 1 23 529 gi|48563 beta-lactamase [Yersinia enterocolitica] 55 38507 1026 1 60 335 gi|47804 Opp C (AA1-301) [Salmonella typhimurium] 5526 276 1525 1 1 282 gi|1477533 sarA [Staphylococcus aureus] 55 29 2821814 2 224 985 gi|1046078 M. genitalium predicted coding region MG369[Mycoplasma genitalium] 55 38 762 3254 1 254 81 gi|413968 ipa-44d geneproduct [Bacillus subtilis] 55 30 174 3695 1 345 4 gi|216773 haloacetatedehalogenase H-1 [Moraxella sp.] 55 32 342 3721 1 1 312 gi|42029 ORF1gene product [Escherichia coli] 55 31 312 3799 1 3 272 gi|42029 ORF1gene product [Escherichia coli] 55 38 270 3889 1 22 423 gi|1129145acetyl-CoA C-acyltransferase [Mangifera indica] 55 45 402 3916 1 2 385gi|529754 speC [Streptococcus pyogenes] 55 38 384 3945 1 4 198 gi|476252phase 1 flagellin [Salmonella enterica] 55 36 195 4074 1 246 4 gi|42029ORF1 gene product [Escherichia coli] 55 38 243 4184 1 2 343 gi|1524267unknown [Hycobacterium tuberculosis] 55 28 342 4284 1 14 208 gi|1100774ferredoxin-dependent glutamate synthase [Synechocystis sp.] 55 36 1954457 2 378 112 gi|180189 cerebellar-degeneration-related antigen (CDR34)[Homo sapiens] gi|182737 55 38 267 cerebellar degeneration-associatedprotein [Homo sapiens] pir|A29770|A29770 cerebellar degeneration-relatedprotein - human 4514 1 2 244 gi|216773 haloacetate dehalogenase H-1[Moraxella sp.] 55 32 243 4599 1 217 2 gi|1129145 acetyl-CoAC-acyltransferase [Mangifera indica] 55 42 216 4606 1 210 4 gi|386120myosin alpha heavy chain (S2 subfragment) [rabbits, masseter, eptide 5527 207 Partial, 234 aa] 5 8 4932 4516 gi|536069 ORF YBL047c[Saccharomyces cerevisiae] 54 27 417 12 7 6165 5164 gi|1205504homoserine acetyltransferase [Haemophilus influenzae] 54 30 1002 23 1615326 13566 gi|474192 iucC gene product [Escherichia coli] 54 31 1761 351 2 979 gi|48054 small subunit of soluble hydrogenase (AA 1-384)[Synechococcus sp.] 54 36 978 ir|S06919|HQYCSS soluble hydrogenase (EC1.12.—.—) small chain - nechococcus sp. (PCC 6716) 37 11 8667 7897gi|537207 ORF_f277 [Escherichia coli] 54 38 771 37 12 8165 8332gi|1160967 palmitoyl-protein thioesterase [Homo sapiens] 54 37 168 46 1513025 13804 gi|438473 protein is hydrophobic, with homology to E. coliProW; putative Bacillus 54 28 780 subtilis] 56 2 203 736 gi|1256139 YbbJ[Bacillus subtilis] 54 34 534 57 13 10179 9241 gi|1151248inosine-uridine preferring nucleoside hydrolase [Crithidia fasciculata]54 32 939 66 2 516 1133 gi|1335781 Cap [Drosophila melanogaster] 54 29618 70 10 8116 8646 gi|1399823 PhoE [Rhizobium meliloti] 54 31 531 70 1511801 11046 sp|P02983|TCR_S TETRACYCLINE RESISTANCE PROTEIN. 54 29 75687 5 4915 5706 gi|1064811 function unknown [Bacillus subtilis] 54 33 79292 4 2289 1573 gi|1205366 oligopeptide transport ATP-binding protein[Haemophilus influenzae] 54 33 717 103 2 1556 516 gi|710495 proteinkinase [Bacillus brevis] 54 33 1041 105 2 2095 605 gi|143727 putative[Bacillus subtilis] 54 30 1491 112 4 2337 2732 gi|153724 MalC[Streptococcus pneumoniae] 54 41 396 127 2 1720 2493 gi|144297 acetylesterase (XynC) [Caldocellum saccharolyticum] pir|B37202|B37202 54 34774 acetylesterase (EC 3.1.1.6) (XynC) - Caldocellum accharolyticum 1385 1600 3306 gi|42473 pyruvate oxidase [Escherichia coli] 54 36 1707 1522 525 1172 gi|1377834 unknown [Bacillus subtilis] 54 23 648 161 9 48315469 gi|903305 ORF73 [Bacillus subtilis] 54 28 639 161 13 6694 7251gi|1511039 phosphate transport system regulatory protein [Methanococcusjannaschii] 54 32 558 164 6 3263 4543 gi|1204976 prolyl-tRNA synthetase[Haemophilus influenzae] 54 34 1281 164 20 21602 22243 gi|143582spoIIIEA protein [Bacillus subtilis] 54 32 642 171 6 4250 2817 gi|436965[malA] gene products [Bacillus stearothermophilus] pir|S43914|S43914 5437 1434 hypothetical protein 1 - Bacillus stearothermophilus 206 1819208 19720 gi|1240016 R09E10.3 [Caenorhabditis elegans] 54 38 513 218 21090 1905 gi|467378 unknown [Bacillus subtilis] 54 26 816 220 1 663 4gi|1353761 myosin II heavy chain [Naegleria fowleri] 54 22 660 220 1312655 13059 pir|S00485|S004 gene 11-1 protein precursor - Plasmodiumfalciparum (fragments) 54 35 405 221 3 2030 3709 gi|1303813 YqeW[Bacillus subtilis] 54 34 1680 272 7 4219 3383 gi|62964 arylamineN-acetyltransferase (AA 1-290) [Gallus gallus] ir|S06652|XYCHY3 54 33837 arylamine N-acetyltransferase (EC 2.3.1.5) (clone NAT-3) - chicken316 7 4141 4701 gi|682769 mccE gene product [Escherichia coli] 54 31 561316 10 6994 8742 gi|413951 ipa-27d gene product [Bacillus subtilis] 5428 1749 338 3 2214 1051 gi|490328 LORF F [unidentified] 54 28 1164 341 43201 3614 gi|171959 myosin-like protein [Saccharomyces cerevisiae] 54 25414 346 1 912 4 gi|396400 similar to eukaryotic Na+/H+ exchangers[Escherichia coli] 54 34 909 sp|P32703|YJCE_ECOLI HYPOTHETICAL 60.5 KDPROTEIN IN SOXR-ACS NTERGENIC REGION (0549). 348 2 623 1351 gi|537109ORF_f343a [Escherichia coli] 54 34 729 378 2 1007 1942 sp|P02983|TCR_STETRACYCLINE RESISTANCE PROTEIN 54 31 936 408 6 4351 5301 gi|474190 iucAgene product [Escherichia coli] 54 29 951 444 9 7934 8854 gi|216267 ORF2[Bacillus megaterium] 54 32 921 463 2 2229 1741 gi|304160 productunknown [Bacillus subtilis] 54 50 489 502 2 1133 570 gi|1205015hypothetical protein (SP: P10120) [Haemophilus influenzae] 54 38 564 5056 5357 4452 gi|1500558 2-hydroxyhepta-2,4-diene-1,7-dioate isomerase[Methanococcus jannaschii] 54 41 906 550 1 1522 308 gi|40100 rodC (tag3)polypeptide (AA 1-746) [Bacillus subtilis] ir|S06049|S06049 54 35 1215rodC protein - Bacillus subtilis p|P13485|TAGF_BACSU TECHOIC ACIDBIOSYNTHESIS PROTEIN F. 551 5 3305 4279 gi|950197 unknown[Corynebacterium glutamicum] 54 34 975 558 2 958 560 gi|485090 Nodefinition line found [Caenorhabditis elegans] 54 32 399 580 1 91 936gi|331906 fused envelope glycoprotein precursor [Friend spleenfocus-forming irus] 54 45 846 603 3 554 757 gi|1323423 ORF YGR234w[Saccharomyces cerevisiae] 54 36 204 617 1 25 249 gi|219959 ornithinetranscarbamylase [Homo sapiens] 54 40 225 622 3 1097 1480 gi|1303873YqgZ [Bacillus subtilis] 54 25 384 623 1 3 404 gi|1063250 low homologyto P20 protein of Bacillus lichiniformis and bleomycin 54 45 402acetyltransferase of Streptomyces verticillus [Bacillus subtilis] 689 11011 475 gi|552446 NADH dehydrogenase subunit 4 [Apis melliferaligustica]pir|S52968|S52968 54 30 537 NADH dehydrogenase chain 4 -honeybee itochondrion (SGC4) 725 2 686 1441 gi|987096 sensory proteinkinase [Streptomyces hygroscopicus] 54 26 756 956 1 1 249pir|S30782|S307 integrin homolog - yeast [Saccharomyces cerevisiae] 5424 249 978 2 859 581 gi|1301994 ORF YNL091w [Saccharomyces cerevisiae]54 33 279 1314 1 3 281 gi|1001108 hypothetical protein [Synechocystissp.] 54 33 279 2450 1 1 228 gi|1045057 ch-TOG [Homo sapiens] 54 32 2282934 1 1 387 gi|580870 ipa-37d qoxA gene product [Bacillus subtilis] 5436 387 2970 1 251 3 sp|P37348|YECE_(—) HYPOTHETICAL PROTEIN IN ASPS5′REGION (FRAGMENT). 54 42 249 3002 1 1 309 gi|44027 Tma protein[Lactococcus lactis] 54 33 309 3561 1 9 464 gi|151259 HMG-CoA reductase(EC 1.1.1.88) [Pseudomonas mevalonii] pir|A44756|A44756 54 35 456hydroxymethylglutaryl-CoA reductase (EC 1.1.1.88) Pseudomonas sp. 3572 172 401 gi|450688 hsdM gene of EcoprrI gene product [Escherichia coli]pir|S38437|S38437 hsdM 54 36 330 protein - Escherichia colipir|S09629|S09629 hypothetical protein A - Escherichia coli (SUB 40-520)3829 1 400 2 gi|1322245 mevalonate pyrophosphate decarboxylase [Rattusnorvegicus] 54 29 399 3909 1 1 273 gi|29865 CENP-E [Homo sapiens] 54 30273 3921 1 3 209 pir|S24325|S243 glucan 1,4-beta-glucosidase (EC3.2.1.74) - Pseudomonas fluorescens subsp. 54 34 207 cellulosa 4438 1285 4 gi|1196657 unknown protein [Mycoplasma pneumoniae] 54 30 282 44591 3 272 gi|1046081 hypothetical protein (GB: D26185_10) [Mycoplasmagenitalium] 54 38 270 4564 1 3 221 gi|216267 ORF2 [Bacillus megaterium]54 38 219 23 12 10685 8832 gi|474192 iucC gene product [Escherichiacoli] 53 35 1854 23 14 13579 12317 gi|42029 ORF1 gene product[Escherichia coli] 53 32 1263 24 3 3940 3440 gi|1369947 c2 gene product[Bacteriophage B1] 53 36 501 26 4 3818 4618 gi|1486247 unknown [Bacillussubtilis] 53 37 801 38 6 2856 3998 gi|405880 yeil [Escherichia coli] 5340 1143 38 10 7806 6232 gi|1399954 thyroid sodium/iodide symporter NIS[Rattus norvegicus] 53 29 1575 56 10 12100 11876 pir|A54592|A545 110kactin filament-associated protein - chicken 53 32 225 57 6 4583 4119pir|A00341|DEZP alcohol dehydrogenase (EC 1.1.1.1) - fission yeast[Schizosaccharomyces 53 39 465 pombe] 57 12 8932 7349 gi|1480429putative transcriptional regulator [Bacillus stearothermophilus] 53 301584 67 12 9496 10218 gi|1511555 quinolone resistance norA proteinprotein [Methanococcus jannaschii] 53 31 723 69 3 2382 1639 gi|1087017arabinogalactan-protein, AGP [Nicotiana alata, cell-suspension culture53 30 744 filtrate, Peptide, 461 aa] 79 1 3 1031 gi|1523802 glucanase[Anabaena variabilis] 53 32 1029 80 1 338 3 gi|452428 ATPase 3[Plasmodium falciparum] 53 36 336 88 4 1910 2524 gi|537034 ORF_o488[Escherichia coli] 53 25 615 88 5 2467 3282 gi|537034 ORF_o488[Escherichia coli] 53 29 816 92 8 5505 5140 gi|399598 amphotropic murineretrovirus receptor [Rattus norvegicus] 53 33 366 94 5 3239 2061gi|173038 tropomyosin (TPM1) [Saccharomyces cerevisiae] 53 25 1179 99 54207 5433 sp|P28246|BCR_E BICYCLOMYCIN RESISTANCE PROTEIN (SULFONAMIDERESISTANCE PROTEIN) 53 30 1227 120 3 1639 2262 gi|576655 ORF1 [Vibrioanguillarum] 53 35 624 120 11 7257 8897 gi|1524397 glycine betainetransporter OpuD [Bacillus subtilis] 53 33 1641 127 6 5685 4477gi|1256630 putative [Bacillus subtilis] 53 32 1209 147 2 255 557gi|581648 epiB gene product [Staphylococcus epidermidis] 53 34 303 158 44256 3807 gi|151004 mucoidy regulatory protein AlgR [Pseudomonasaeruginosa] pir|A32802|A32802 53 32 450 regulatory protein algR—Pseudomonas aeruginosa sp|P26275|ALGR_PSEAE POSITIVE ALGINATEBIOSYNTHESIS REGULATORY ROTEIN. 171 7 5421 5125 gi|1510669 hypotheticalprotein (GP: D64044_18) [Methanococcus jannaschii] 53 34 297 191 9 114839879 gi|298085 acetoacetate decarboxylase [Clostridium acetobutylicum]pir|B49346|B49346 53 31 1605 butyrate—acetoacetate CoA-transferase (EC.8.3.9) small chain - Clostridium acetobutylicum sp|P33752|CTFA_CLOABBUTYRATE-ACETOACETATE COA- TRANSFERASE SUBUNIT (EC 2.8.3.9) (COAT A) 2035 3763 4326 gi|143456 rpoE protein (ttg start codon) [Bacillus subtilis]53 29 564 206 17 18204 18971 gi|304136 acetylglutamate kinase [Bacillusstearothermophilus] sp|Q07905|ARGB_BACST 53 36 768 ACETYLGLUTAMATEKINASE (EC 2.7.2.8) (NAG INASE) (AGK) (N-ACETYL-L- GLUTAMATE5-PHOSPHOTRANSFERASE). 212 10 4021 4221 gi|9878 protein kinase[Plasmodium falciparum] 53 28 201 231 2 1350 1120 gi|537506 paramyosin[Dirofilaria immitis] 53 34 231 272 6 2719 3249 pir|A33141|A331hypothetical protein (gtfD 3′ region) - Streptococcus mutans 53 34 531308 3 927 2576 gi|606292 ORF_o696 [Escherichia coli] 53 33 1650 320 75645 5884 gi|160596 RNA polymerase III largest subunit [Plasmodiumfalciparum] 53 33 240 sp|P27625|RPC1_PLAFA DNA-DIRECTED RNA POLYMERASEIII LARGEST UBUNIT (EC 2.7.7.6). 327 1 218 901 gi|854601 unknown[Schizosaccharomyces pombe] 53 31 684 341 2 212 2500 gi|633732 ORF1[Campylobacter jejuni] 53 31 2289 351 1 383 3 sp|P31675|YABM_(—)HYPOTHETICAL 42.7 KD PROTEIN IN TBPA-LEUD INTERGENIC REGION (ORF104). 5332 381 433 7 4731 4375 gi|1001961 MHC class II analog [Staphylococcusaureus] 53 30 357 454 2 980 720 pir|A60328|A603 40K cell wall proteinprecursor (sr 5′ region) - Streptococcus mutans 53 27 261 (strainOMZ175, serotype f) 470 4 1123 1761 gi|516826 rat GCP360 [Rattus rattus]53 30 639 483 1 217 2 gi|1480429 putative transcriptional regulator[Bacillus stearothermophilus] 53 33 216 544 1 516 1259 gi|46587 ORF 1(AA 1-121) (1 is 2nd base in codon) [Staphylococcus aureus] 53 38 744ir|S15765|S15765 hypothetical protein 1 (hlb 5′ region) - Staphylococcusaureus (fragment) 558 10 3754 3551 gi|15140 res gene [Bacteriophage P1]53 32 204 603 2 339 620 gi|507738 Hmp [Vibrio parahaemolyticus] 53 26282 693 1 941 213 gi|153123 toxic shock syndrome toxin-1 precursor[Staphylococcus aureus] 53 38 729 pir|A24606|XCSAS1 toxic shock syndrometoxin-1 precursor - Staphylococcus aureus 766 1 2 673 gi|687600 orfA2;orfA2 forms an operon with orfA1 [Listeria monocytogenes] 53 43 672 7811 335 3 gi|1204551 pilin biogenesis protein [Haemophilus influenzae] 5326 333 801 1 3 545 gi|1279400 SapA protein [Escherichia coli] 53 25 543803 1 2 910 gi|695278 lipase-like enzyme [Alcaligenes eutrophus] 53 30909 872 1 590 3 gi|298032 EF [Streptococcus suis] 53 30 588 910 1 2 184gi|1044936 unknown [Schizosaccharomyces pombe] 53 29 183 943 1 399 4gi|290508 similar to unidentified ORF near 47 minutes [Escherichia coli]53 30 396 sp|P31436|YICK_ECOLI HYPOTHETICAL 43.5 KD PROTEIN IN SELC-NLPANTERGENIC REGION. 988 1 504 4 gi|142441 ORF 3; putative [Bacillussubtilis] 53 28 501 1064 1 3 434 gi|305080 myosin heavy chain [Entamoebahistolytica] 53 26 432 1366 1 3 452 gi|308852 transmembrane protein[Lactococcus lactis] 53 33 450 1758 1 397 2 gi|1001774 hypotheticalprotein [Synechocystis sp.] 53 30 396 1897 1 1 447 gi|1303949 YqiX[Bacillus subtilis] 53 27 447 2381 1 400 2 gi|1146243 22.4% identitywith Escherichia coli DNA-damage inducible protein ...; 53 37 399putative [Bacillus subtilis] 3537 1 1 327 gi|450688 hsdM gene of EcoprrIgene product [Escherichia coli] pir|S38437|S38437 hsdM 53 35 327protein - Escherichia coli pir|S09629|S09629 hypothetical protein A -Escherichia coli [SUB 40-520] 3747 2 137 397 gi|1477486 transposase[Burkholderia cepacia] 53 53 261 11 5 3049 3441 gi|868224 No definitionline found [Caenorhabditis elegans] 52 33 393 15 5 2205 2369 gi|215966G41 protein (gtg start codon) [Bacteriophage T4] 52 34 165 19 3 24293808 gi|1205379 UDP-murnac-pentapeptide synthetase [Haemophilusinfluenzae] 52 31 1380 24 1 3462 4 gi|579124 predicted 86.4 kd protein;52 Kd observed [Mycobacteriophage 15] 52 32 3459 pir|S30971|S30971 gene26 protein - Mycobacterium phage L5 sp|Q05233|VG26_BPML5 MINOR TAILPROTEIN GP26. (SUB 2-837) 37 5 3015 3935 gi|1500543 P115 protein[Methanococcus jannaschii] 52 25 921 38 13 8795 9703 gi|46851 glucosekinase [Streptomyces coelicolor] 52 29 909 44 16 10617 11066 gi|42012moaE gene product [Escherichia coli] 52 36 450 46 1 3 521 gi|1040957NADH dehydrogenase subunit 6 [Anopheles trinkae] 52 25 519 51 10 55316280 gi|388269 traC [Plasmid pAD1] 52 32 750 56 5 2826 1684 gi|181949endothelial differentiation protein (edg-1) [Homo sapiens] 52 23 1143pir|A35300|A35300 G protein-coupled receptor edg-1 - humansp|P21453|EDG1_HUMAN PROBABLE G PROTEIN-COUPLED RECEPTOR EDG-1. 57 54173 3496 gi|304153 sorbitol dehydrogenase [Bacillus subtilis] 52 27 67862 5 2870 2376 gi|1072399 phaE gene product [Rhizobium meliloti] 52 25495 62 6 3651 2857 gi|46485 NADH dehydrogenase [Synechococcus PCC7942]52 27 795 67 14 11355 12962 gi|1511365 glutamate synthase (NADPH),subunit alpha [Methanococcus jannaschii] 52 30 1608 67 21 16935 18158gi|1204393 hypothetical protein (SP: P31122) [Haemophilus influenzae] 5225 1224 70 4 1997 1809 gi|7227 cytoplasmic dynein heavy chain[Dictyostelium discoldeum]r|A44357|A44357 52 36 189 dynein heavy chain,cytosolic - slime mold Dictyostelium discoideum) 96 10 10005 10664gi|1408485 B65G gene product [Bacillus subtilis] 52 26 660 103 5 33512716 gi|1009368 Respiratory nitrate reductase [Bacillus subtilis] 52 42636 109 3 3350 2598 gi|699274 lmbE gene product [Mycobacterium leprae]52 39 753 109 19 15732 17300 gi|1526981 amino acid permease YeeF likeprotein [Salmonella typhimurium] 52 30 1569 121 3 981 550 gi|732931unknown [Saccharomyces cerevisiae] 52 32 432 125 3 865 1680 gi|1296975puT gene product [Porphyromonas gingivalis] 52 38 816 130 2 659 1807gi|1256634 25.8% identity over 120 aa with the Synenococcus sp. MpeVprotein; putative 52 36 1149 [Bacillus subtilis] 149 1 583 2 gi|1225943PBSX terminase [Bacillus subtilis] 52 33 582 149 14 4415 4143 gi|1510368M. jannaschii predicted coding region MJ0272 [Methanococcus jannaschii]52 35 273 167 1 216 1001 gi|146025 cell division protein [Escherichiacoli] 52 43 786 188 1 120 1256 gi|474915 orf 337; translated orfsimilarity to SW: BCR_ECOLI bicyclomycin esistance 52 26 1137 protein ofEscherichia coli [Coxiella burnetii] pir|S44207|S44207 hypotheticalprotein 337 - Coxiella burnetii (SUB -338) 195 9 8760 8359 gi|3028mitochondrial outer membrane 72K protein [Neurospora crassa] 52 25 402r|A36682|A36682 72K mitochondrial outer membrane protein - Neurosporacrassa 200 3 2065 2607 gi|142439 ATP-dependent nuclease [Bacillussubtilis] 52 35 543 203 4 2776 3684 gi|303698 BltD [Bacillus subtilis]52 25 909 227 8 5250 5651 gi|305080 myosin heavy chain [Entamoebahistolytica] 52 24 402 242 1 21 1424 gi|1060877 EmrY [Escherichia coli]52 32 1404 249 5 4526 4753 pir|C37222|C372 cytochrome P450 1A1,hepatic - dog (fragment) 52 23 228 255 1 1055 3 gi|143290penicillin-binding protein [Bacillus subtills] 52 28 1053 276 7 36643365 gi|1001610 hypothetical protein [Synechocystis sp.] 52 30 300 276 84055 3654 gi|416235 orf L3 [Mycoplasma capricolum] 52 26 402 289 2 14491042 gi|150900 GTP phosphohydrolase [Proteus vulgaris] 52 34 408 325 1 1279 gi|1204874 polypeptide deformylase (formylmethionine deformylase)[Haemophilus 52 33 279 influenzae] 340 1 1010 3 gi|1215695 peptidetransport system protein SapF homolog; SapF homolog [Mycoplasma 52 331008 pneumoniae] 375 3 340 1878 gi|467446 similar to SpoVB [Bacillussubtilis] 52 28 1539 424 4 3262 2420 gi|1478239 unknown [Mycobacteriumtuberculosis] 52 34 843 430 1 3 575 pir|A42606|A426 orfA 5′ to orf405 -Saccharopolyspora erythraea (fragment) 52 28 573 444 4 3712 2696gi|1408494 homologous to penicillin acylase [Bacillus subtilis] 52 311017 465 1 903 4 gi|143331 alkaline phosphatase regulatory protein[Bacillus subtilis] 52 36 900 pir|A27650|A27650 regulatory proteinphoR - Bacillus subtilis sp|P23545|PHOR_BACSU ALKALINE PHOSPHATASESYNTHESIS SENSOR PROTEIN HOR (EC 2.7.3.—) 469 5 4169 3633 gi|755152highly hydrophobic integral membrane protein [Bacillus subtilis] 52 32537 sp|P42953|TAGG_BACSU TEICHOIC ACID TRANSLOCATION PERMEASE PROTEINAGG. 495 1 633 4 gi|1204607 transcription activator [Haemophilusinfluenzae] 52 25 630 505 7 5762 5520 gi|142440 ATP-dependent nuclease[Bacillus subtilis] 52 28 243 517 2 1162 1614 gi|166162 Bacteriophagephi-11 int gene activator [Staphylococcus acteriophage phi 52 35 453 11]543 2 444 1295 gi|1215693 putative orf; GT9_orf434 [Mycoplasmapneumoniae] 52 25 852 586 1 1 336 gi|581648 epiB gene product[Staphylococcus epidermidis] 52 36 336 773 1 426 4 gi|1279769 FdhC[Methanobacterium thermofomicicum] 52 30 423 1120 2 100 330 gi|142439ATP-dependent nuclease [Bacillus subtilis] 52 35 231 1614 1 347 3gi|289262 comE ORF3 [Bacillus subtilis] 52 28 345 2495 1 1 324 gi|216151DNA polymerase (gene L; ttg start codon) [Bacteriophage SP02] gi|57919752 34 324 SP02 DNA polymerase (aa 1-648) [Bacteriophage SPO2]pir|A21498|DJBPS2 DNA- directed DNA polymerase (EC 2.7.7.7) - phage PO22931 1 285 4 gi|1256136 YbbG [Bacillus subtilis] 52 30 282 2943 1 320 63gi|41713 hisA ORF (AA 1-245) [Escherichia coli] 52 35 258 2993 1 295 2gi|298032 EF [Streptococcus suis] 52 34 294 3667 1 307 2 gi|849025hypothetical 64.7-kDa protein [Bacillus subtilis] 52 36 306 3944 1 26042 gi|1218040 BAA [Bacillus licheniformis] 52 36 219 3954 2 347 81gi|854064 U87 [Human herpesvirus 6] 52 50 267 3986 1 90 401 gi|1205919Na+ and Cl− dependent gamma-aminobutryic acid transporter [Haemophilus52 33 312 influenzae] 4002 1 3 389 gi|40003 oxoglutarate dehydrogenase(NADP+) [Bacillus subtilis] p|P23129|ODO1_BACSU 52 42 387 2-OXOGLUTARATEDEHYDROGENASE E1 COMPONENT (EC 2.4.2) (ALPHA-KETOGLUTARATEDEHYDROGENASE). 4020 1 1 249 gi|159388 ornithine decarboxylase[Leishmania donovani] 52 47 249 4098 1 220 2 gi|409795 No definitionline found [Escherichia coli] 52 32 219 4248 1 3 212 gi|965077 Adr6p[Seccharomyces cerevisiae] 52 40 210 7 1 3 575 gi|895747 putative celoperon regulator [Bacillus subtilis] 51 28 573 21 4 2479 3276 gi|1510962indole-3-glycerol phosphate synthase [Methanococcus jannaschii] 51 32798 22 9 5301 5966 gi|1303933 YqiN [Bacillus subtilis] 51 25 666 43 31283 1050 gi|1519460 Srp1 [Schizosaccharomyces pombe] 51 31 234 44 1711042 11305 gi|42011 moaD gene product [Escherichia coli] 51 35 264 5111 6453 6731 gi|495471 vacuolating toxin [Helicobacter pylori] 51 37 27952 4 2537 2995 gi|1256652 25% identity to the E. coli regulatory proteinMprA; putative [Bacillus 51 32 459 subtilis] 57 10 6843 6355 gi|508173EIIA domain of PTS-dependent Gat transport and phosphorylationEscherichia 51 32 489 coli] 59 1 29 1111 gi|299163 alanine dehydrogenase[Bacillus subtilis] 51 33 1083 67 20 15791 16576 gi|1510977 M.jannaschii predicted coding region MJ0938 [Methanococcus jannaschii] 5124 786 69 2 1218 877 gi|467359 unknown [Bacillus subtilis] 51 34 342 711 3 1196 gi|298032 EF [Streptococcus suis] 51 32 1194 78 2 176 3gi|1161242 proliferating cell nuclear antigen [Styela clava] 51 28 17499 4 3357 4040 gi|642795 TFIID subunit TAFII55 [Homo sapiens] 51 25 684109 1 1428 4 gi|580920 rodD (gtaA) polypeptide (AA 1-673) [Bacillussubtilis] pir|S06048|S06048 51 27 1425 probable rodD protein - Bacillussubtilis sp|P13484|TAGE_BACSU PROBABLE POLY (GLYCEROL-PHOSPHATE)LPHA-GLUCOSYLTRANSFERASE (EC 2.4.1.52) (TECHOIC ACID BIOSYNTHESIS ROTEINE) 109 9 6007 6693 gi|1204815 hypothetical protein (SP: P32662)[Haemophilus influenzae] 51 23 687 112 3 1066 2352 pir|S05330|S053maltose-binding protein precursor - Enterobacter aerogenes 51 42 1287112 13 12855 11278 gi|405857 yehU [Escherichia coli] 51 29 1578 114 98967 8209 gi|435098 orf1 [Mycoplasma capricolum] 51 30 759 115 1 1 912gi|1431110 ORF YDL085w [Saccharomyces cerevisiae] 51 25 912 127 10 964710477 gi|1204314 H. influenzae predicted coding region HI0056[Haemophilus influenzae] 51 37 831 152 9 6814 7356 gi|431929 MunIregulatory protein [Mycoplasma sp.] 51 38 543 154 2 575 1153 gi|1237044unknown [Mycobacterium tuberculosis] 51 36 579 154 7 5634 4681 gi|409286bmrU [Bacillus subtilis] 51 27 954 171 8 6236 5529 gi|1205484hypothetical protein (SP: P33918) [Haemophilus influenzae] 51 32 708 1841 1 291 gi|466886 B1496_C3_206 [Mycobacterium leprae] 51 33 291 212 51501 2139 pir|A45605|A456 mature-parasite-infected erythrocyte surfaceantigen MESA - Plasmodium 51 23 639 falciparum 228 2 707 1378 gi|8204nuclear protein [Drosophila melanogaster] 51 27 672 236 8 7481 6825gi|49272 Asparaginase [Bacillus licheniformis] 51 31 657 243 4 3546 2455gi|1511102 melvalonate kinase [Methanococcus jannaschii] 51 29 1092 2574 3373 3206 gi|1204579 H. influenzae predicted coding region HI0326[Haemophilus influenzae] 51 22 168 258 3 1609 821 gi|160299 glutamicacid-rich protein [Plasmodium falciparum] pir|A54514|A54514 51 34 789glutamic acid-rich protein precursor - Plasmodium falciparum 265 5 24193591 gi|580841 F1 [Bacillus subtilis] 51 32 1173 298 2 518 748gi|1336162 SCPB [Streptococcus agalactiae| 51 34 231 316 9 5817 7049gi|413953 ipa-29d gene product [Bacillus subtilis] 51 39 1233 332 2 2057339 gi|1209012 mutS [Thermus aquaticus thermophilus] 51 26 1719 364 43816 4991 gi|528991 unknown [Bacillus subtilis] 51 32 1176 440 2 448 684gi|2819 transferase (GAL10) (AA 1-687) [Kluyveromyces lactis]r|S01407|XUVKG 51 32 237 UDPglucose 4-epimerase (EC 5.1.3.2) - yeastuyveromyces marxianus var. lactis) 495 2 1177 1001 gi|297861 protease G[Erwinia chrysanthemi] 51 41 177 495 3 1718 1149 gi|1513317 serine richprotein [Entamoeba histolytica] 51 25 570 506 1 421 2 gi|455320 cIIprotein [Bacteriophage P4] 51 33 420 600 1 983 492 gi|587532 orf, len:201, CAI: 0.16 [Saccharomyces cerevisiae] pir|S48818|S48818 51 30 492hypothetical protein - yeast (Saccharomyces erevisiae) 607 3 479 934gi|1511524 hypothetical protein (SP: P37002) [Methanococcus jannaschii]51 40 456 686 2 127 600 gi|493017 endocarditis specific antigen[Enterococcus faecalis] 51 30 474 726 1 33 230 gi|1353851 unknown[Prochlorococcus marinus] 51 45 198 861 1 176 652 gi|410145dehydroquinate dehydratase [Bacillus subtilis] 51 34 477 869 1 393 4gi|40100 rodC (tag3) polypeptide (AA 1-746) [Bacillus subtilis]ir|S06049|S06049 51 23 390 rodC protein - Bacillus subtilisp|P13485|TAGF_BACSU TECHOIC ACID BIOSYNTHESIS PROTEIN F. 1003 1 322 2gi|1279707 hypothetical phosphoglycerate mutase [Saccharomycescerevisiae] 51 39 321 1046 2 624 382 gi|510257 glycosyltransferase[Escherichia coli] 51 29 243 1467 1 352 2 gi|1511175 M. jannaschiipredicted coding region MJ1177 [Methanococcus jannaschii] 51 32 351 25581 230 3 sp|P10582|DPOM_(—) DNA POLYMERASE (EC 2.7.7.7) (S-1 DNA ORF 3).51 26 228 3003 1 399 19 gi|809543 CbrC protein [Erwinia chrysanthemi] 5127 381 3604 1 1 399 pir|JC4210|JC42 3-hydroxyacyl-CoA dehydrogenase (EC1.1.1.35) - mouse 51 37 399 3732 1 2 316 gi|145906 acyl-CoA synthetase[Escherichia coli] 51 33 315 3791 1 2 274 gi|1061351 semaphorin IIIfamily homolog [Homo sapiens] 51 37 273 3995 1 46 336 gi|216346surfactin synthetase [Bacillus subtilis] 51 38 291 4193 1 307 2 gi|42749ribosomal protein L12 (AA 1-179) [Escherichia coli] ir|S04776|XXECPL 5125 306 peptide N-acetyltransferase rimL (EC 2.3.1.—) - Echerichia coli4539 1 185 3 gi|1408494 homologous to penicillin acylase [Bacillussubtilis] 51 40 183 4562 1 239 36 gi|1458280 coded for by C. eleganscDNA cm01e7; Similar to hydroxymethylglutaryl-CoA 51 35 204 synthase[Caenorhabditis elegans] 1 4 3576 4859 gi|559160 GRAIL score: null; capsite and late promoter motifs present pstream; 50 44 1284 putative[Autographa californica nuclear polyhedrosis irus] 11 7 4044 5165gi|1146207 putative [Bacillus subtilis] 50 35 1122 11 13 9496 8483gi|1208451 hypothetical protein [Synechocystis sp.] 50 39 1014 19 1 10182 gi|413966 ipa-42d gene product [Bacillus subtilis] 50 29 1017 20 118407 8228 gi|1323159 ORF YGR103w [Saccharomyces cerevisiae] 50 28 180 245 4824 4240 gi|496280 structural protein [Bacteriophage Tuc2009] 50 29585 34 4 1926 2759 gi|1303966 Yqj0 [Bacillus subtilis] 50 36 834 38 3022865 23440 gi|1072179 Similar to dihydroflavonol-4-reductase (maize,petunia, tomato) 50 32 576 [Caenorhabditis elegans] 47 2 1705 2976gi|153015 FemA protein [Staphylococcus aureus] 50 29 1272 56 13 1529015841 gi|606096 ORF_f167; end overlaps end of o100 by 14 bases; startoverlaps f174, ther 50 30 552 starts possible [Escherichia coli] 57 11077 19 gi|640922 xylitol dehydrogenase (unidentified hemiascomycete) 5029 1059 58 2 628 1761 gi|143725 putative [Bacillus subtilis] 50 29 113488 6 3884 3375 gi|1072179 Similar to dihydroflavonol-4-reductase (maize,petunia, tomato) 50 32 510 [Caenorhabditis elegans] 89 5 3356 3012gi|1276658 ORF174 gene product [Porphyra purpurea] 50 25 345 141 1 3 239gi|476024 carbamoyl phosphate synthetase II [Plasmodium falciparum] 5033 237 151 1 186 626 gi|1403441 unknown [Mycobacterium tuberculosis] 5035 441 166 7 9623 8181 gi|895747 putative cel operon regulator [Bacillussubtilis] 50 32 1443 201 6 5096 4908 gi|160229 circumsporozoite protein[Plasmodium reichenowi] 50 42 189 206 22 29555 28326 gi|1052754 LmrPintegral membrane protein [Lactococcus lactis] 50 24 1230 211 4 15231927 gi|410131 ORFX7 [Bacillus subtilis] 50 29 405 214 4 2411 3295sp|P37348|YECE_(—) HYPOTHETICAL PROTEIN IN ASPS 5′ REGION (FRAGMENT) 5037 885 228 7 4406 3744 gi|313580 envelope protein [Humanimmunodeficiency virus type 1] pir|S35835|S35835 50 35 663 envelopeprotein - human immunodeficiency virus type 1 (fragment) (SUB 1- 77) 2722 1723 398 gi|1408485 B65G gene product [Bacillus subtilis] 50 22 1326273 2 984 352 gi|984186 phosphoglycerate mutase [Saccharomycescerevisiae] 50 28 633 328 2 1605 703 gi|148896 lipoprotein [Haemophilusinfluenzae] 50 26 903 332 4 3802 2135 gi|1526547 DNA polymerase family X[Thermus aquaticus] 50 27 1668 342 5 3473 3931 gi|456562 G-box bindingfactor [Dictyostelium discoideum] 50 35 459 352 1 741 4 gi|288301 ORF2gene product [Bacillus megaterium] 50 29 738 408 7 5299 5523 gi|11665ORF2136 [Marchantia polymorpha] 50 27 225 420 3 650 1825 gi|757842UDP-sugar hydrolase [Escherichia coli] 50 30 1176 464 1 1 591 gi|487282Na+ -ATPase subunit J [Enterococcus hirae] 50 29 591 472 2 864 310gi|551875 Bg1R [Lactococcus lactis] 50 23 555 520 1 23 541 gi|567036CapE [Staphylococcus aureus] 50 27 519 529 1 6 410 gi|1256652 25%identity to the E. coli regulatory protein MprA; putative [Bacillus 5034 405 subtilis] 534 5 6059 4392 gi|295671 selected as a weak suppressorof a mutant of the subunit AC40 of DNA 50 18 1668 ependant RNApolymerase I and III [Saccharomyces cerevisiae] 647 1 1497 4 gi|405568TraI protein shares sequence similarity with a family of opoisomerases50 31 1494 [Plasmid pSK41] 664 3 711 289 gi|410007 leukocidin Fcomponent [Staphylococcus aureus, MRSA No. 4, Peptide, 23 aa] 50 32 423678 1 1 627 gi|298032 EF [Streptococcus suis] 50 29 627 755 3 947 1171gi|150572 cytochrome c1 precursor (EC 1.10.2.2) [Paracoccusdenitrificans] gi|45465 50 37 225 cytochrome c1 (AA 1-450) [Paracoccusdenitrificans] pir|C29413|C29413 ubiquinol - cytochrome-c reductase (EC1.10.2.2) ytochrome c1 precursor - Paracoccus denitrificanssp|P13627|CY1 827 1 683 3 gi|142020 heterocyst differentiation protein[Anabaena sp.] 50 21 681 892 1 3 752 gi|1408485 B65G gene product[Bacillus subtilis] 50 27 750 910 2 438 887 gi|1204727 tyrosine-specifictransport protein [Haemophilus influenzae] 50 25 450 933 1 524 760gi|1205451 cell division inhibitor [Haemophilus influenzae] 50 32 237973 1 236 48 gi|886947 orf3 gene product [Saccharomyces cerevisiae] 5040 189 1009 1 429 205 gi|153727 M protein [group G streptococcus] 50 28225 1027 1 257 3 gi|413934 ipa-10r gene product [Bacillus subtilis] 5025 255 1153 2 326 96 gi|773676 nccA [Alcaligenes xylosoxydans] 50 36 2311222 1 400 2 gi|1408485 B65G gene product [Bacillus subtilis] 50 21 3991350 1 399 106 gi|289272 ferrichrome-binding protein [Bacillus subtilis]50 32 294 2945 1 184 2 gi|171704 hexaprenyl pyrophosphate synthetase(COQ1) [Saccharomyces erevisiae] 50 34 183 2968 2 804 4 gi|397526clumping factor [Staphylococcus aureus] 50 33 801 2998 2 394 131gi|495696 F54E7.3 gene product [Caenorhabditis elegans] 50 40 264 3046 2306 106 pir|S13819|S138 acyl carrier protein - Anabaena variabilis(fragment) 50 32 201 3063 1 275 3 gi|474190 iucA gene product[Escherichia coli] 50 29 273 3174 1 3 146 gi|151900 alcoholdehydrogenase [Rhodobacter sphaeroides] 50 31 144 3792 1 314 3gi|1001423 hypothetical protein [Synechocystis sp.] 50 35 312 3800 1 2262 gi|144733 NAD-dependent beta-hydroxybutyryl coenzyme A dehydrogenaseClostridium 50 28 261 acetobutylicum] 3946 1 188 3 gi|576765 cytochromeb [Myrmecia pilosula] 50 38 186 3984 1 291 4 sp|P37348|YECE_(—)HYPOTHETICAL PROTEIN IN ASPS 5′ REGION (FRAGMENT). 50 37 288 37 10 78857520 gi|1204367 hypothetical protein (GB: U14003_278) [Haemophilusinfluenzae] 49 30 366 46 16 13802 14848 gi|466860 acd: B1308_F1_34[Mycobacterium leprae] 49 24 1047 59 5 2267 3601 gi|606304 ORF_o462[Escherichia coli] 49 27 1335 112 18 17884 18615 gi|559502 ND4 protein(AA 1-409) [Caenorhabditis elegans] 49 25 732 138 9 6973 7902 gi|303953esterase [Acinetobacter calcoaceticus] 49 29 930 217 6 4401 5138gi|496254 fibronectin/fibrinogen-blnding protein [Streptococcuspyogenes] 49 31 738 220 12 11803 12657 gi|397526 clumping factor[Staphylococcus aureus] 49 31 855 228 4 1842 2492 pir|S23692|S236hypothetical protein 9 - Plasmodium falciparum 49 24 651 268 1 2614 212gi|143047 ORFB [Bacillus subtilis] 49 26 2403 271 2 1164 1373 gi|1001257hypothetical protein [Synechocystis sp.] 49 38 210 300 3 3180 2020gi|1510796 hypothetical protein (GP: X91006_2) [Methanococcusjannaschii] 49 26 1161 381 1 1142 3 gi|396301 matches PS00041: Bacterialregulatory proteins, araC family ignature 49 29 1140 [Escherichia coli]466 1 3 947 gi|1303863 YqgP [Bacillus subtilis] 49 26 945 666 1 191 3gi|633112 ORF1 [Streptococcus sobrinus] 49 29 189 670 2 403 1014gi|1122758 unknown [Bacillus subtilis] 49 32 612 709 1 795 157 gi|143830xpaC [Bacillus subtilis] 49 29 639 831 1 473 3 gi|401786phosphomannomutase [Mycoplasma pirum] 49 29 471 1052 1 213 4 gi|1303799YqeN [Bacillus subtilis] 49 21 210 1800 1 172 2 gi|216300 peptidoglycansynthesis enzyme [Bacillus subtilis] sp|P37585|MURG_BACSU 49 28 171 MURGPROTEIN UPD-N-ACETYLGLUCOSAMINE—N-ACETYLMURAMYL- PENTAPEPTIDE)PYROPHOSPHORYL-UNDECAPRENOL N-ACETYLGLUCOSAMINE RANSFERASE). 2430 1 2376 sp|P27434|YFGA_(—) HYPOTHETICAL 36.2 KD PROTEIN IN NDK-GCPEINTERGENIC REGION. 49 26 375 3096 1 273 4 gi|516360 surfactin synthetase[Bacillus subtilis] 49 25 270 32 4 3100 2429 gi|1217963 hepatocytenuclear factor 4 gamma (HNF4gamma) [Homo sapiens] 48 36 672 38 1 1 609gi|1205790 H. influenzae predicted coding region HI1555 [Haemophilusinfluenzae] 48 28 609 45 6 5021 6427 gi|1524267 unknown [Mycobacteriumtuberculosis] 48 20 1407 59 14 16346 31096 gi|1197336 Lmp3 protein[Mycoplasma hominis] 48 28 14751 61 1 3 608 gi|1511555 quinoloneresistance norA protein protein [Methanococcus jannaschii] 48 30 606 613 3311 3646 gi|1303893 YqhL [Bacillus subtilis] 48 29 336 114 1 98 415gi|671708 su(s) homolog; similar to Drosophila melanogaster suppressorof able 48 25 318 (su(s)) protein, Swiss-Prot Accession Number P22293Drosophila virilis) 121 1 610 89 gi|1314584 unknown [Sphingomonas S88]48 29 522 136 1 1280 546 gi|1205968 H. influenzae predicted codingregion HI1738 [Haemophilus influenzae] 48 23 735 171 10 8220 9557gi|1208454 hypothetical protein [Synechocystis sp.] 48 34 1338 175 11814 3 gi|396400 similar to eukaryotic Na+/H+ exchangers [Escherichiacoli] 48 29 1812 sp|P32703|YJCE_ECOLI HYPOTHETICAL 60.5 KD PROTEIN INSOXR-ACS NTERGENIC REGION (O549). 194 1 2 385 gi|1510493 M. jannaschiipredicted coding region MJ0419 [Methanococcus jannaschii] 48 25 384 1971 452 3 gi|1045714 spermidine/putrescine transport ATP-binding protein[Mycoplasma genitalium] 48 25 450 203 1 1 396 gi|940288 proteinlocalized in the nucleoli of pea nuclei; ORF; putative Pisum 48 29 396sativum] 204 1 698 33 gi|529202 No definition line found [Caenorhabditiselegans] 48 25 666 206 20 27760 20705 gi|511490 gramicidin S synthetase2 [Bacillus brevis] 48 27 7056 212 1 2 166 gi|295899 nucleolin [Xenopuslaevis] 48 34 165 220 10 11426 10200 gi|44073 SecY protein [Lactococcuslactis] 48 23 1227 243 6 5491 4532 gi|1184118 mevalonate kinase[Methanobacterium thermoautotrophicum] 48 30 960 264 4 3308 1182gi|1015903 ORF YJR151c [Saccharomyces cerevisiae] 48 26 2127 441 1 768 4gi|142863 replication initiation protein [Bacillus subtilis]pir|B26580|B26580 48 23 765 replication initiation protein - Bacillussubtilis 444 5 3898 5298 gi|145836 putative [Escherichia coli] 48 241401 484 2 388 1110 gi|146551 transmembrane protein (kdpD) [Escherichiacoli] 48 18 723 542 3 1425 2000 pir|S28969|S289 N-carbamoylsarcosineamidohydrolase (EC 3.5.1.59) - Arthrobacter sp. 48 27 576 566 1 3 1019gi|153490 tetracenomycin C resistance and export protein [Streptomyceslaucescens] 48 24 1017 611 1 2 730 gi|1103507 unknown[Schizosaccharomyces pombe] 48 38 729 624 1 665 75 gi|144859 ORF B[Clostridium perfringens] 48 26 591 846 1 508 2 gi|537506 paramyosin[Dirofilaria immitis] 48 27 507 1020 1 66 950 gi|1499876 magnesium andcobalt transport protein [Methanococcus jannaschii] 48 30 885 1227 1 1174 gi|493730 lipoxygenase [Pisum sativum] 48 35 174 1266 1 1 405gi|882452 ORF_f211; alternate name yggA; orf5 of X14436 [Escherichiacoli] gi|41425 48 24 405 ORF5 (AA 1-197) [Escherichia coli] (SUB 15-211)2071 1 381 55 gi|1408486 HS74A gene product [Bacillus subtilis] 48 25327 2398 1 233 3 gi|1500401 reverse gyrase [Methanococcus jannaschii] 4840 231 2425 1 246 16 pir|H48563|H485 G1 protein - fowlpox virus (strainHP444) (fragment) 48 40 231 2432 1 225 4 gi|1353703 Trio [Homo sapiens]48 33 222 2453 1 399 4 gi|142850 division initiation protein [Bacillussubtilis] 48 29 396 2998 1 236 3 gi|577569 PepV [Lactobacillusdelbrueckii] 48 31 234 3042 1 14 280 gi|945219 mucin [Homo sapiens] 4835 267 3686 1 1 405 gi|145836 putative [Escherichia coli] 48 25 405 40272 301 110 pir|S51177|S511 trans-activator protein - Equine infectiousanemia virus 48 32 192 4 2 2232 823 gi|1303989 YqkI [Bacillus subtilis]47 24 1410 24 2 599 1084 gi|540083 PC4-1 gene product [Bradysia hygida]47 28 486 36 10 6925 6326 gi|1209223 esterase [Acinetobacter lwoffii] 4726 600 43 2 196 1884 gi|1403455 unknown [Mycobacterium tuberculosis] 4727 1689 44 22 15108 14098 gi|1511555 quinolone resistance norA proteinprotein [Methanococcus jannaschii] 47 31 1011 69 7 6710 6279 gi|438466Possible operon with orfG. Hydrophilic, no homologue in the atabase; 4729 432 putative [Bacillus subtilis] 81 4 4279 3536 gi|466882 ppsl;B1496_C2_189 [Mycobacterium leprae] 47 24 744 120 12 8863 8591 gi|927340D9509.27p; CAI: 0.12 [Saccharomyces cerevisiae] 47 38 273 142 1 1174 326gi|486143 ORF YKL094w [Saccharomyces cerevisiae] 47 32 849 168 1 1093 8gi|1177254 hypothetical EcsB protein [Bacillus subtilis] 47 29 1086 2631 943 2 gi|142822 D-alanine racemase cds [Bacillus subtilis] 47 34 942279 1 561 13 gi|516608 2 predicted membrane helices, homology with B.subtilis men Orf3 Rowland 47 31 549 et. al. unpublished Accession numberM74183), approximately 1 minutes on updated Rudd map; putative[Escherichia coli] sp|P37355|YFBB_ECOLI HYPOTHETICAL 26.7 KD PROTEIN INMEND-MENB 345 2 1676 732 gi|1204835 hippuricase [Haemophilus influenzae]47 28 945 389 2 152 400 gi|456562 G-box binding factor [Dictyosteliumdiscoideum] 47 32 249 391 1 1 831 gi|1420856 myo-inositol transporter[Schizosaccharomyces pombe] 47 19 831 404 3 2072 2773 gi|1255425 C33G8.2gene product [Caenorhabditis elegans] 47 17 702 529 5 2145 3107gi|1303973 YqjV [Bacillus subtilis] 47 29 963 565 2 1257 193 gi|142824processing protease [Bacillus subtilis] 47 28 1065 654 1 483 4 gi|243353ORF 5′ of ECRF3 [herpesvirus saimiri HVS, host-squirrel monkey, eptide,407 47 23 480 aa] 692 1 115 633 gi|150756 40 kDa protein [Plasmid pJM1]47 25 519 765 1 819 4 gi|1256621 26.7% of identity in 165 aa to aThermophilic bacterium hypothetical 47 28 816 protein 6; putative[Bacillus subtilis] 825 2 211 1023 gi|397526 clumping factor[Staphylococcus aureus] 47 32 813 914 1 1 615 gi|558073 polymorphicantigen [Plasmodium falciparum] 47 29 615 1076 1 1 753 gi|1147557Aspartate aminotransferase [Bacillus circulans] 47 33 753 1351 1 398 3gi|755153 ATP-binding protein [Bacillus subtilis] 47 20 396 4192 1 3 293gi|145836 putative [Escherichia coli] 47 24 291 5 6 4361 4014 gi|305080myosin heavy chain [Entamoeba histolytica] 46 30 348 11 4 2777 3058gi|603639 Ye1040p [Saccharomyces cerevisiae] 46 28 282 46 11 10300 10082gi|1246901 ATP-dependent DNA ligase [Candida albicans] 46 28 219 61 43941 7930 gi|298032 EF [Streptococcus suis] 46 35 3990 132 4 4093 3158gi|1511057 hypothetical protein SP: P45869 [Methanococcus jannaschii] 4625 936 170 4 3652 2585 pir|S51910|S519 G4 protein - sauroleishmaniatarentolae 46 26 1068 191 7 8284 7025 gi|1041334 F54D5.7 [Caenorhabditiselegans] 46 25 1260 253 1 1 396 gi|1204449 dihydrolipoamideacetyltransferase [Haemophilus influenzae] 46 35 396 264 3 437 973gi|180189 cerebellar-degeneration-related antigen (CDR34) [Homo sapiens]gi|182737 46 29 537 cerebellar degeneration-associated protein [Homosapiens] pir|A29770|A29770 cerebellar degeneration-related protein -human 273 1 285 85 gi|607573 envelope glycoprotein C2V3 region [Humanimmunodeficiency virus type] 46 35 201 350 1 3 563 gi|537052 ORF_E286[Escherichia coli] 46 35 561 384 1 2 862 gi|1221884 (urea?) amidolyase[Haemophilus influenzae] 46 31 861 410 4 1876 2490 gi|1110518 protonantiporter efflux pump [Mycobacterium smegmatis] 46 24 615 432 1 1455247 gi|1197634 orf4; putative transporter; Method: conceptualtranslation supplied by 46 27 1209 author [Mycobacterium smegmatis] 4581 1211 3 gi|15470 portal protein [Bacteriophage SPP1] 46 30 1209 517 52477 4192 gi|1523812 orf5 [Bacteriophage A2] 46 23 1716 540 3 1285 1058gi|215635 pacA [Bacteriophage P1] 46 30 228 587 2 649 1242 gi|537148ORF_f181 [Escherichia coli] 46 29 594 1218 1 391 35 gi|1205456single-stranded-DNA-specific exonuclease [Haemophilus influenzae] 46 30357 3685 1 1 402 gi|450688 hsdM gene of EcoprrI gene product[Escherichia coli] pir|S38437|S38437 hsdM 46 33 402 protein -Escherichia coli pir|S09629|S09629 hypothetical protein A - Escherichiacoli (SUB 40-520) 4176 1 338 3 gi|951460 FIM-C.1 gene product [Xenopuslaevis] 46 31 336 37 7 4813 5922 gi|606064 ORF_f408 [Escherichia coli]45 24 1110 38 16 11699 12004 gi|452192 protein tyrosine phosphatase(PTP-BAS, type 2) [Homo sapiens] 45 24 306 87 2 1748 2407 gi|1064813homologous to sp: PHOR_BACSU [Bacillus subtilis] 45 23 660 103 12 1338512588 gi|1001307 hypothetical protein [Synechocystis sp.] 45 22 798 11214 13811 12831 gi|1204389 H. influenzae predicted coding region HI0131[Haemophilus influenzae] 45 23 981 145 4 3461 2439 gi|220578 openreading frame [Mus musculus] 45 20 1023 170 6 4965 3601 gi|238657 AppC =cytochrome d oxidase, subunit I homolog [Escherichia coli, K12, 45 271365 eptide, 514 aa] 206 2 4346 3462 gi|1222056 aminotransferase[Haemophilus influenzae] 45 27 885 228 1 60 716 gi|160299 glutamicacid-rich protein [Plasmodium falciparum] pir|A54514|A54514 45 23 657glutamic acid-rich protein precursor - Plasmodium alciparum 288 1 2 1015gi|1255425 C33G8.2 gene product [Caenorhabditis elegans] 45 23 1014 3133 3128 1917 gi|581140 NADH dehydrogenase [Escherichia coli] 45 30 1212332 1 459 4 gi|870966 F47A4.2 [Caenorhabditis elegans] 45 20 456 344 1 3221 gi|171225 kinesin-related protein [Saccharomyces cerevisiae] 45 26219 441 2 1073 645 gi|142863 replication initiation protein [Bacillussubtilis] pir|B26580|B26580 45 27 429 replication initiation protein -Bacillus subtilis 672 1 2 982 gi|1511334 M. jannaschii predicted codingregion MJ1323 [Methanococcus jannaschii] 45 22 981 763 3 851 357gi|606180 ORF_f310 [Escherichia coli] 45 24 495 886 3 379 846 gi|726426similar to protein kinases and C. elegans proteins F37C12.8 and 37C12.545 30 468 [Caenorhabditis elegans] 948 1 3 473 gi|156400 myosin heavychain (isozyme unc-54) [Caenorhabditis elegans] 45 25 471pir|A93958|MWKW myosin heavy chain B - Caenorhabditis eleganssp|P02566|MYSB_CAEEL MYOSIN HEAVY CHAIN B (MHC B). 1158 1 2 376gi|441155 ransmission-blocking target antigen [Plasmodium falciparum] 4535 375 2551 1 4 285 gi|1276705 ORF287 gene product [Porphyra purpurea]45 28 282 3967 1 42 374 gi|976025 MrsA [Escherichia coli] 45 28 333 52 75846 4761 gi|467378 unknown [Bacillus subtilis] 44 22 1086 138 8 64756849 gi|173028 thioredoxin II [Saccharomyces cerevisiae] 44 28 375 221 55617 4202 gi|153490 tetracenomycin C resistance and export protein[Streptomyces laucescens] 44 21 1416 252 2 1122 913 gi|1204989hypothetical protein (GB: U00022_9) [Haemophilus influenzae] 44 30 210263 2 2093 921 gi|1136221 carboxypeptidase [Sulfolobus solfataricus] 4426 1173 365 4 3524 2085 gi|1296822 orf1 gene product [Lactobacillushelveticus] 44 31 1440 543 3 1315 1833 gi|1063250 low homology to P20protein of Bacillus lichiniformis and bleomycin 44 24 519acetyltransferase of Streptomyces verticillus [Bacillus subtilis] 544 43942 4892 gi|951460 FIM-C.1 gene product [Xenopus laevis] 44 32 951 7921 613 2 gi|205680 high molecular weight neurofilament [Rattusnorveglcus] 44 28 612 44 18 11303 11911 gi|1511614 molybdopterin-guaninedinucleotide biosynthesis protein A [Methanococcus 43 27 609 jannaschii]59 8 3665 5128 gi|153490 tetracenomycin C resistance and export protein[Streptomyces laucescens] 43 21 1464 59 10 5536 7527 gi|153022 lipaseStaphylococcus epidermidis] 43 22 1992 99 1 681 16 gi|1419051 unknown[Mycobacterium tuberculosis] 43 21 666 310 8 9402 12134 gi|397526clumping factor [Staphylococcus aureus] 43 21 2733 432 3 2303 1824pir|A60540|A605 sporozoite surface protein 2 - Plasmodium yoelii(fragment) 43 29 480 519 3 2547 3122 sp|Q06530|DHSU_(—) SULFIDEDEHYDROGENASE (FLAVOCYTOCHROME C) FLAVOPROTEIN CHAIN PRECURSOR (EC 43 23576 1.8.2.—) (FC) (FCSD). 4 13 12053 13321 gi|295671 selected as a weaksuppressor of a mutant of the subunit AC40 of DNA 42 18 1269 ependantRNA polymerase I and III [Saccharomyces cerevisiae] 94 2 1091 414gi|501027 ORF2 [Trypanosoma brucei] 42 31 678 127 4 4550 3309 gi|42029ORF1 gene product [Escherichia coli] 42 21 1242 297 3 1036 557 gi|142790ORF1; putative [Bacillus firmus] 42 25 480 344 6 3525 2953 gi|40320 ORF2 (AA 1-203) [Bacillus thuringiensis] 42 30 573 512 1 1115 63 gi|405957yeeF [Escherichia coli] 42 23 1053 631 1 1223 12 gi|580920 rodD (gtaA)polypeptide (AA 1-673) [Bacillus subtilis] pir|S06048|S06048 42 24 1212probable rodD protein - Bacillus subtilis sp|P13484|TAGE_BACSU PROBABLEPOLY(GLYCEROL-PHOSPHATE) LPHA-GLUCOSYLTRANSFERASE (EC 2.4.1.52) (TECHOICACID BIOSYNTHESIS ROTEIN E). 685 3 1739 1119 gi|1303784 YqeD [Bacillussubtilis] 42 19 621 4132 1 395 3 gi|1022910 protein tyrosine phosphatase[Dictyostelium discoideum] 42 25 393 86 2 884 393 gi|309506spermidine/spermine N1-acetyltransferase [Mus saxicola]pir|S43430|S43430 41 30 492 spermidine/spermine N1-acetyltransferase -spiny ouse (Mus saxicola) 191 12 14075 13353 gi|1124957 orf4 geneproduct [Methanosarcina barkeri] 41 22 723 212 6 2150 3127 gi|15873observed 35.2 Kd protein [Mycobacteriophage 15] 41 26 978 213 3 12632000 gi|633692 TrsA [Yersinia enterocolitica] 41 18 738 408 4 2625 3386gi|1197634 orf4; putative transporter; Method: conceptual translationsupplied by 41 24 762 author [Mycobacterium smegmatis] 542 1 3 1103gi|457146 rhoptry protein [Plasmodium, yoelii] 41 21 1101 924 1 2 475pir|JH0148|JH01 nucleolin - rat 41 30 474 1562 1 1 402 gi|552184asparagine-rich antigen Pfa35-2 [Plasmodium falciparum]pir|S27826|S27826 40 20 402 asparagine-rich antigen Pfa35-2 - Plasmodiumalciparum (fragment) 2395 1 261 4 pir|S42251|S422 hypothetical protein5 - fowlpox virus 40 18 258 4077 1 3 305 gi|1055055 coded for by C.elegans cDNA yk37g1.5; coded for by C. elegans cDNA 39 21 303 yk5c9.5;coded for by C. elegans cDNA yk1a9.5; alternatively spliced form ofF52C9.8b [Caenorhabditis elegans] 958 1 503 3 gi|1255425 C33G8.2 geneproduct [Caenorhabditis elegans] 37 25 501 59 12 8294 10636 gi|535260STARP antigen [Plasmodium reichenowi] 36 24 2343 63 5 3550 8079gi|298032 EF [Streptococcus suis] 36 19 4530 544 3 2507 3601 gi|1015903ORF YJR151c [Saccharomyces cerevisiae] 35 22 1095 63 4 1949 3574gi|552195 circumsporozoite protein (Plasmodium falciparum)sp|P05691|CSP_PLAFL 32 27 1626 CIRCUMSPOROZOITE PROTEIN (CS) (FRAGMENT).

[0290] TABLE 3 S. aureus - Putative coding regions of novel proteins notsimilar to known proteins Contig ORF Start Stop ID ID (nt) (nt) 4 1 692150 4 3 1712 2278 4 4 3032 2361 4 14 12585 12097 5 2 1601 663 5 3 15321771 5 7 4550 4359 5 9 6422 4905 5 12 8547 8383 6 4 1982 1605 8 1 176 311 8 5144 5983 11 9 5968 6498 11 10 6284 6096 11 16 10954 11271 12 54942 4532 12 6 4596 4862 15 3 1650 1405 16 10 10835 10407 18 2 917 74120 9 7764 6403 20 10 8230 7889 20 12 8803 8405 20 13 10470 8782 23 1 3394 23 6 5485 4832 23 8 5942 5508 23 9 6881 6111 23 15 12618 12830 24 44185 3814 24 6 5241 4840 25 2 1824 2402 31 2 505 849 31 3 1177 1524 31 42454 3005 32 2 765 1388 32 9 7952 8575 32 10 8591 8728 32 11 9379 902032 12 10087 9377 34 2 1049 783 36 7 5226 5801 36 11 7261 6947 36 12 74247621 37 4 2964 2770 38 2 980 375 38 11 6425 6868 38 20 16371 15760 38 2620253 20804 38 27 20722 21264 39 1 1 627 40 1 404 3 43 1 428 60 44 42324 1974 44 5 2484 3263 44 14 10129 9671 44 20 13536 13348 44 21 1359613994 45 7 6297 6019 46 8 6365 6520 46 12 10449 10976 46 17 15032 1542447 1 288 1079 48 9 7620 7778 50 1 962 312 50 2 1316 1011 51 1 370 2 51 52245 1970 53 1 287 132 53 7 6319 5933 54 7 8709 8404 55 1 326 60 55 3786 520 56 1 1 261 56 3 1228 905 56 4 1560 1150 56 17 18712 18332 57 43521 3348 57 8 5436 5822 58 9 8553 8221 59 3 1366 1509 59 6 2802 2578 597 3570 3370 59 9 4563 4180 59 11 7518 8378 59 13 10401 16403 62 2 1521346 62 11 5440 5757 63 1 1 336 67 1 900 1781 67 2 1774 2610 67 3 25913904 67 8 6955 6800 68 1 78 326 70 6 5199 3637 70 11 8645 8355 77 3 1192794 79 2 1228 947 79 3 1411 1791 83 1 2 403 85 9 8300 8653 85 10 87818593 86 3 1232 1038 87 8 9187 9366 88 3 1620 1922 89 1 3 161 89 7 48784714 91 1 550 2 91 3 3141 2344 92 2 449 928 92 3 1467 976 92 9 5638 602494 1 332 3 94 3 1813 1181 94 4 2197 1811 96 11 10601 11050 99 6 45234374 99 7 4784 4554 100 8 7287 6916 102 7 4368 4039 103 3 2035 1574 1041 2 694 104 2 699 1277 105 1 693 151 105 3 2655 2077 106 1 3 221 106 31209 1355 107 1 542 3 109 4 3651 3277 109 13 11625 11996 109 14 1198112268 109 20 17401 17688 110 1 2 760 114 10 8764 9384 116 1 1 309 116 34462 2651 116 8 9976 8903 116 9 10158 10003 120 5 3320 2937 120 6 38693468 120 13 9290 9844 121 2 417 569 126 3 818 546 127 3 2648 3196 127 54084 4395 131 6 6438 6103 132 2 715 1695 134 1 2 667 135 2 258 4 135 3729 334 138 1 3 152 138 7 6008 6463 140 1 1032 4 140 2 1513 1007 140 52387 2743 142 2 1360 2388 142 7 7586 6342 143 7 6502 5714 144 1 640 53146 1 2 511 146 3 502 1350 146 4 2540 1407 146 5 2874 3071 147 1 1 339149 11 3615 3274 149 12 3785 3534 149 13 4145 3783 149 15 4610 4413 14916 5049 4603 149 18 5491 5243 149 21 7054 6692 149 23 8521 7826 149 249106 8531 149 25 9897 9115 150 2 1587 871 154 3 1508 1221 154 8 63986210 154 14 12147 11590 154 15 12803 12075 156 1 315 593 157 3 1183 2232158 2 1064 657 159 3 452 808 161 2 876 1808 161 6 4279 3905 161 7 45404277 161 8 4717 4538 161 11 5638 5459 163 2 840 76 163 5 2344 1892 163 72647 2342 163 9 4905 5132 164 3 1147 956 166 3 4854 4495 168 4 2500 2868168 5 3595 4158 170 3 2517 2777 171 2 1450 623 171 11 11125 9674 172 1 3278 172 2 1149 358 173 1 708 127 173 5 6114 5227 174 2 593 1105 175 32552 2890 175 5 3335 2850 175 7 4342 4506 182 4 4986 4495 184 5 57025361 188 2 1210 1755 188 4 2647 2994 189 6 2614 3039 190 3 1998 2564 1911 1 153 191 2 669 388 191 10 11786 13039 191 11 12363 11824 192 1 91 426195 3 1932 1558 195 5 2606 2313 198 2 1016 1591 201 1 170 625 203 2 7831466 206 6 7815 6700 206 12 13636 13325 206 21 27960 27712 212 2 170 817212 3 796 1167 212 7 3128 3436 212 9 3749 4075 213 1 1 705 214 2 570 64214 6 3738 3412 214 9 6600 6995 214 10 7469 7074 217 1 965 3 218 1 178657 218 3 1776 2156 220 2 1369 887 220 3 2262 1273 220 7 7208 6141 220 88661 7078 220 9 10216 8636 221 4 2613 2131 221 9 10757 10086 226 1 3 659226 2 1459 722 226 3 1476 1961 227 1 2 487 227 2 460 975 227 4 1855 2121227 5 2052 2345 227 6 3768 2776 227 9 5591 6367 228 5 2503 2877 228 62846 3526 233 7 3762 3580 236 2 579 349 238 2 1391 807 239 2 905 393 2415 4334 4173 242 2 1363 1049 243 1 127 576 244 1 647 3 244 2 1962 889 2452 1258 902 246 1 69 215 246 4 738 1733 249 3 3712 3518 250 1 249 4 254 11 156 256 2 956 1144 257 3 3227 2754 260 4 4580 4254 261 4 2196 2606 2616 3214 3681 264 2 155 439 264 5 4533 3814 264 6 4739 5107 267 2 931 539268 4 4700 4260 272 1 446 30 272 3 1200 1439 272 9 4691 4909 272 10 60355601 276 4 1746 1901 278 1 224 553 278 5 3299 3448 278 7 4849 5127 285 2551 736 288 3 1756 1950 288 5 2055 2276 289 1 1055 3 290 2 1932 1630 2912 332 622 291 5 1545 2051 295 3 1349 1092 295 4 2141 1554 295 5 22202762 297 2 465 142 298 1 2 205 300 2 1928 1476 301 7 2624 2454 304 1 3194 306 1 109 654 306 5 4036 4257 307 1 339 4 307 8 3645 3995 308 1 1654 308 2 599 78 308 4 2332 2021 313 2 1919 1524 314 1 10 702 316 2 9821341 316 6 2758 3165 317 1 2 1114 317 3 3458 2346 321 6 5217 4789 321 76140 5961 321 8 6794 6138 322 2 543 259 326 2 165 1112 326 3 1117 1467328 1 469 2 328 5 3276 3100 329 1 3 719 329 2 781 1212 329 3 1471 1833330 1 289 2 330 3 1447 1623 332 3 2204 2055 332 7 4971 5138 333 2 31282961 335 1 433 2 337 2 95 526 340 2 1356 1054 341 1 3 281 341 3 24763192 341 5 3618 3944 341 6 3929 4558 344 5 2889 2581 345 1 768 4 346 2221 592 350 3 1410 1598 352 2 1765 1352 352 3 4596 1876 352 7 7967 8404352 8 8906 9247 352 9 9854 9537 359 1 1 546 362 1 3 656 364 2 1808 1458364 8 10714 10454 365 2 1313 1014 365 5 4090 3500 365 7 4980 6239 366 3520 1719 367 3 906 1085 368 1 494 240 375 1 2 136 380 3 1097 843 389 1 1276 390 1 2 877 390 2 1373 1549 391 2 560 369 395 1 197 3 396 1 1068 4398 3 1141 938 399 1 178 669 401 3 566 847 402 2 100 465 404 8 5370 5179408 2 2269 1031 408 3 2672 2469 408 5 3524 4423 410 3 1890 1669 413 1488 96 416 1 320 33 416 2 578 847 416 3 1590 985 417 1 3 179 417 2 161616 420 2 513 238 422 2 357 677 431 2 856 1407 432 2 446 1084 433 1 1417 433 3 2033 1755 434 1 535 128 434 2 1235 381 440 1 1 450 442 2 12693320 443 3 1520 1167 444 1 1 696 444 7 6366 5971 451 1 614 288 453 2 636376 453 8 3833 4786 453 9 4512 4306 453 10 4731 4525 455 1 219 4 455 2472 930 459 1 265 687 462 1 2 247 466 2 907 320 467 1 349 44 468 1 2 250469 1 925 362 469 3 2386 3372 469 4 3464 3706 470 1 77 538 470 6 36943290 470 7 5686 5042 470 9 7351 8181 470 10 8175 9773 471 1 500 60 471 21017 472 476 1 70 267 477 1 2 760 477 3 1764 2081 477 4 2066 2332 480 54016 4261 481 2 480 4 486 3 613 774 487 6 1795 2112 488 1 359 3 492 1127 675 493 1 2 520 493 2 496 1242 502 3 1149 1571 504 1 346 2 505 54150 3734 511 2 1232 723 512 2 583 747 515 1 609 812 517 4 2179 2511 5204 2097 2360 520 6 3669 3430 527 1 1 498 528 1 335 33 529 2 1104 529 5307 5298 5534 536 1 156 4 538 1 736 110 538 3 2203 2880 538 5 3121 2711538 6 3731 3114 540 1 664 332 540 2 1031 567 541 1 89 433 541 2 432 145542 2 1048 1272 545 2 734 456 551 1 1129 113 555 2 704 516 558 3 1154951 558 4 1458 1156 558 5 1821 1537 558 6 2020 1874 558 7 2322 2008 5588 2802 2551 558 9 3453 2920 560 1 475 921 565 3 1485 1264 571 1 156 4571 3 994 1206 577 1 2 199 577 2 163 453 579 1 1 477 579 2 1200 616 5831 996 4 585 1 539 132 587 1 22 573 588 2 1372 848 588 3 1554 1366 590 147 334 592 2 1141 827 593 1 2 775 593 2 817 1122 595 1 87 890 596 3 14351277 602 1 8 169 603 5 1071 1469 606 1 322 768 607 5 1226 1008 610 1 54153 612 1 3 500 616 1 650 309 617 2 491 246 622 1 36 347 625 4 2046 2549627 1 67 210 628 1 452 3 631 3 4004 3219 634 1 759 70 636 1 189 368 6362 1063 197 637 2 1994 1665 638 1 227 1081 639 1 261 4 639 2 811 245 6411 118 444 642 3 1331 1047 642 4 1847 1434 643 1 3 608 645 4 1534 1758645 6 2025 2321 645 7 2488 2036 648 1 2 1045 660 1 77 601 660 2 576 872661 1 961 197 664 2 89 304 667 1 3 413 668 1 1 330 671 2 516 220 673 1 3338 674 2 584 303 679 1 1 237 679 3 1589 1906 688 1 835 434 688 2 1077802 694 1 3 143 696 2 432 46 706 1 224 81 709 3 1183 1449 711 1 3 908715 1 3 167 716 1 2 637 721 1 133 570 722 1 383 3 723 1 829 2 723 2 1112726 727 1 2 472 729 1 268 441 731 1 130 828 735 1 2 214 736 1 3 782 7381 2 298 742 1 3 230 745 3 780 412 748 2 282 464 749 1 344 3 751 1 452 3755 1 97 522 755 2 520 918 758 2 400 137 764 2 746 459 767 1 1 405 768 12 373 771 1 534 10 778 1 902 69 785 1 1023 256 787 1 631 2 791 1 3 224799 1 15 260 804 1 304 711 805 1 3 680 808 1 219 842 810 1 1112 3 810 21442 1110 812 1 38 979 817 1 358 2 818 2 487 1104 819 2 1032 535 819 31419 1090 820 1 195 1064 828 1 255 4 829 1 48 800 830 1 291 4 832 1 2982 835 1 320 796 840 3 491 709 845 1 457 2 850 2 303 449 853 1 359 3 8601 2 256 864 1 18 410 864 2 383 715 864 6 1676 1828 870 1 1 588 873 1 4542 875 1 294 4 877 1 1020 379 878 1 544 107 879 1 785 3 881 1 1 243 882 1389 604 890 1 2 508 905 1 398 3 906 1 544 236 912 1 188 3 913 1 3 290913 2 547 2 915 1 6 161 915 2 169 402 921 1 126 386 927 1 808 38 928 1 2385 929 1 2 400 932 1 2 400 934 1 1 384 936 1 528 4 937 1 2 616 945 1220 645 945 2 649 1242 946 1 950 198 949 1 1 270 951 1 3 362 955 1 3 143960 1 400 77 963 1 1 162 965 1 346 2 966 1 606 133 969 1 3 302 971 1 12170 974 1 161 3 976 1 348 4 977 1 2 211 982 1 982 38 984 1 296 3 987 1 3467 993 1 1 525 994 1 549 178 1004 1 318 79 1014 1 313 2 1015 1 2 4631016 1 145 2 1019 1 660 115 1022 1 474 109 1024 1 299 3 1024 2 276 4311030 1 338 3 1032 1 179 3 1040 1 399 4 1043 1 3 269 1044 2 115 399 10471 1 159 1051 1 354 4 1051 2 733 233 1063 1 2 400 1069 1 2 148 1069 2 533297 1075 1 399 91 1077 1 97 405 1081 1 58 438 1086 1 1 384 1087 2 246431 1088 1 3 374 1096 1 238 2 1098 1 509 3 1100 1 511 2 1100 2 1158 7961101 1 353 3 1102 1 194 3 1107 1 2 580 1114 1 3 422 1115 1 2 268 1119 122 267 1129 1 40 342 1132 1 181 2 1133 1 376 143 1144 1 225 4 1147 1 2802 1153 1 1 153 1154 1 3 818 1159 1 1 330 1161 1 186 31 1164 1 254 811171 1 19 240 1171 2 108 299 1183 1 2 379 1195 1 179 3 1196 1 1 189 12001 33 197 1203 2 129 464 1222 2 105 401 1232 1 1 387 1240 1 2 175 1247 1311 102 1271 1 221 30 1286 1 2 595 1295 1 1 165 1306 1 185 3 1314 2 158631 1316 1 58 570 1359 1 193 2 1370 1 1 402 1371 1 1 345 1374 1 357 41378 1 2 400 1392 1 3 413 1411 1 202 432 1433 1 167 3 1450 1 2 256 14531 149 3 1471 1 398 75 1477 1 639 409 1502 1 399 4 1518 1 126 449 1534 1143 3 1546 1 3 401 1547 1 255 4 1583 1 3 350 1587 1 3 563 1602 2 170 6791629 1 1 402 1665 1 235 2 1760 1 314 3 1762 1 3 200 1876 2 119 286 18951 2 379 1931 1 400 2 1976 2 383 51 2055 2 252 401 2056 1 167 3 2150 1263 3 2157 1 399 4 2164 1 283 2 2175 1 218 400 2212 1 331 170 2338 1 3672 2342 1 3 167 2352 1 166 2 2352 2 398 174 2355 1 47 352 2356 1 341 32359 1 152 3 2421 1 150 4 2422 1 306 43 2443 1 263 99 2454 1 3 158 24631 253 2 2485 1 3 374 2557 1 246 4 2575 1 2 355 2582 1 3 284 2607 1 1 2942930 1 17 400 2939 1 242 18 2944 1 3 359 2945 2 399 97 2952 1 2 190 29531 399 61 2964 1 166 2 2969 1 144 4 2977 1 2 373 2981 2 334 167 2986 1 7279 2991 1 363 118 2995 1 1 321 3007 1 191 39 3017 1 308 48 3018 2 136351 3025 1 197 3 3040 1 180 4 3046 1 185 3 3049 1 278 3 3050 1 3 3143052 1 253 2 3065 1 2 157 3070 1 190 23 3075 1 222 4 3080 1 1 285 3092 1162 4 3093 1 250 89 3100 1 52 237 3103 1 47 298 3118 1 174 4 3123 1 2145 3127 1 1 147 3138 1 169 2 3142 1 203 18 3144 1 386 108 3151 1 170 33155 2 202 384 3168 1 12 176 3205 1 145 2 3282 1 1 150 3303 2 239 4003371 2 211 399 3558 1 2 148 3558 2 36 401 3568 1 377 3 3595 1 380 3 36181 2 238 3618 2 130 402 3622 1 86 358 3622 2 398 132 3642 1 439 2 3649 1398 15 3651 1 314 3 3664 1 467 637 3674 1 55 402 3677 1 311 3 3704 1 1402 3726 1 269 3 3765 1 256 2 3779 1 357 160 3794 1 135 4 3794 2 377 873796 2 375 112 3801 1 262 50 3806 1 298 143 3807 1 42 389 3815 1 400 23827 1 3 320 3842 1 392 3 3853 1 399 127 3855 1 1 324 3857 1 2 235 38611 297 4 3865 1 399 103 3897 1 3 173 3897 2 143 400 3898 2 225 401 3921 2103 342 3927 1 70 375 3930 1 76 234 3946 2 382 113 3951 2 105 377 3965 1344 42 3973 1 400 5 3981 1 3 311 3998 1 3 356 4001 1 296 111 4003 1 90335 4018 1 2 259 4018 2 186 401 4021 1 1 345 4043 1 3 344 4054 1 3 3444066 1 1 150 4070 1 1 324 4072 2 187 390 4073 1 1 285 4077 2 127 3724083 1 3 359 4090 1 27 368 4101 1 103 297 4105 1 1 306 4107 1 286 2 41191 339 49 4121 1 372 4 4123 1 3 230 4127 1 3 341 4128 1 2 331 4130 1 41562 4146 1 97 381 4157 1 3 206 4186 1 254 3 4224 1 256 2 4239 1 1 3484242 1 356 3 4252 1 296 3 4253 1 1 174 4256 1 323 78 4258 2 334 170 42671 144 4 4271 1 2 304 4287 1 163 23 4289 1 319 167 4302 1 153 305 4304 11 186 4304 2 96 314 4306 1 2 151 4318 1 289 2 4322 1 5 148 4331 1 221 34331 2 364 200 4338 1 399 70 4346 1 277 83 4367 2 117 311 4373 1 2 2684381 1 326 78 4384 1 309 4 4397 1 9 311 4402 1 1 249 4403 1 328 50 44061 3 317 4411 1 2 280 4411 2 398 99 4412 1 2 364 4418 1 3 230 4424 1 398195 4443 1 215 3 4471 1 323 3 4478 1 271 2 4482 1 50 289 4489 1 302 34491 1 12 206 4495 1 3 179 4496 1 252 4 4500 1 130 306 4511 1 248 3 45181 1 246 4526 1 241 2 4527 1 2 163 4532 1 3 239 4542 1 11 175 4567 1 36200 4573 1 1 231 4578 1 322 2 4619 1 1 180 4620 1 176 3 4662 1 1 2464669 1 2 157 4680 1 28 183 4690 1 174 4

[0291]

0 SEQUENCE LISTING The patent application contains a lengthy “SequenceListing” section. A copy of the “Sequence Listing” is available inelectronic form from the USPTO web site(http://seqdata.uspto.gov/sequence.html?DocID=20040043037). Anelectronic copy of the “Sequence Listing” will also be available fromthe USPTO upon request and payment of the fee set forth in 37 CFR1.19(b)(3).

What is claimed is:
 1. An isolated polynucleotide comprising a nucleicacid fragment of the Staphylococcus aureus genome, wherein said fragmentconsists of the nucleotide sequence of any one of SEQ ID NOS: 1-5,191 asdepicted in Tables 2 and
 3. 2. A vector comprising the polynucleotide ofclaim
 1. 3. An organism which has been altered to contain thepolynucleotide of claim
 1. 4. An isolated polypeptide encoded by any oneof the fragments of the Staphylococcus aureus genome of SEQ ID NOS:1-5,191 and depicted in Tables 2 and
 3. 5. An antibody whichspecifically binds the polypeptide of claim
 4. 6. An isolatedpolynucleotide encoding the polypeptide of claim
 4. 7. A vectorcomprising the polynucleotide of claim
 6. 8. An organism which has beenaltered to contain the polynucleotide of claim
 6. 9. A method forproducing a polypeptide in a host cell comprising the steps of: (a)incubating a host containing a heterologous nucleic acid molecule whosenucleotide sequence consists of the polynucleotide of claim 6 underconditions where said heterologous nucleic acid molecule is expressed toproduce said polypeptide, and (b) isolating said polypeptide.
 10. Anisolated polypeptide comprising an amino acid sequence identical to aStaphylococcus aureus polypeptide amino acid sequence selected from thegroup consisting of SEQ ID NOS: 5,192 to 5,255.